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EASY rewrite

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This commit is contained in:
Bryan Roessler
2024-07-23 10:54:58 -04:00
parent 0440912859
commit 811a1c2dc4
26 changed files with 5472 additions and 167 deletions
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176
workflow/script-run-workflow
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@@ -247,7 +247,8 @@ install_dependencies() {
depends_brew=(graphiz pandoc gd pdftk-java shdoc nano rsync)
depends_perl=(File::Map ExtUtils::PkgConfig GD GO::TermFinder)
depends_r=(BiocManager ontologyIndex ggrepel tidyverse sos openxlsx ggplot2
plyr extrafont gridExtra gplots stringr plotly ggthemes pandoc rmarkdown)
plyr extrafont gridExtra gplots stringr plotly ggthemes pandoc rmarkdown
plotly htmlwidgets)
depends_bioc=(org.Sc.sgd.db)
[[ $1 == "--get-depends" ]] && return 0 # if we just want to read the depends vars
@@ -341,6 +342,10 @@ init_project() {
module easy
# @section EASY
# @description Start an EASY analysis
# Eliminated EstartConsole.m
# TODO Don't create output in the scans folder, put it in an output directory
# TODO The !!Results output files need standardized naming
# TODO Don't perform directory operations in EASY
# * The QHTCPImageFolders and 'MasterPlateFiles' folder are the inputs for image analysis with EASY software.
# * EASY will automatically generate a 'Results' directory (within the ExpJobs/'ExperimentJob' folder) w/ timestamp and an optional short description provided by the user (Fig.2).
# * The 'Results' directory is created and entered, using the "File >> New Experiment" dropdown in EASY.
@@ -400,9 +405,34 @@ module easy
# * When finished, the '!!ResultsStd_.txt' will be about the same file size and it should be used in the following StudiesQHTCP analysis.
# * 'NoGrowth_.txt', and 'GrowthOnly_.txt' files will be generated in the 'PrintResults' folder.
#
# Issues:
# * We need full documentation for all of the current workflow. There are different documents that need to be integrated. This will need to be updated as we make improvements to the system.
# * MasterPlate_ file must have ydl227c in orf column, or else it Z_interaction.R will fail, because it can’t calculate shift values.
# * Make sure there are no special characters; e.g., (), “, ‘, ?, etc.; dash and underscore are ok as delimiters
# * Drug_Media_ file must have letter character to be read as ‘text’.
# * MasterPlate_ file and DrugMedia_ are .xlsx or .xls, but !!Results_ is .txt.
# * In Z_interactions.R, does it require a zero concentration/perturbation (should we use zero for the low conc, even if it’s not zero), e.g., in order to do the shift correctly.
# * Need to enable all file types (not only .xls) as the default for GenerateResults (to select MP and DM files as .xlsx).
# * Explore differences between the ELR and STD files - 24_0414; John R modified Z script to format ELR file for Z_interactions.R analysis.
# * To keep time stamps when transferring with FileZilla, go to the transfer drop down and turn it on, see https://filezillapro.com/docs/v3/advanced/preserve-timestamps/
# * Could we change the ‘MasterPlateFiles’ folder label in EASY to ‘MasterPlate_DrugMedia’ (since there should be only one MP and there is also a DM file required?
# * I was also thinking of adding a ‘MasterPlateFilesOnly’ folder to the QHTCP directory template where one could house different MPFiles (e.g., with and without damps, with and without Refs on all MPs, etc; other custom MPFiles, updated versions, etc)
# * Currently updated files are in ‘23_1011_NewUpdatedMasterPlate_Files’ on Mac (yeast strains/23_0914…/)
# * For EASY to report cell array positions (plate_row_column) to facilitate analyzing plate artifacts. The MP File in Col 3 is called ‘LibraryLocation’ and is reported after ‘Specifics’ in the !!Results.
# * Can EASY/StudiesQ-HTCP be updated at any time by rerunning with updated MP file (new information for gene, desc, etc)- or maybe better to always start with a new template?
# * Need to be aware of file formatting to avoid dates (e.g., with gene names like MAY24, OCT1, etc, and with plate locations 1E1, 1E2, etc)- this has been less of a problem.
# * In StudiesQHTCP folders, remember to annotate Exp1, Exp2, in the StudyInfo.csv file.
# * Where are gene names called from for labeling REMc heatmaps, TSHeatmaps, Z-interaction graphs, etc? Is this file in the QHTCP ‘code’ folder, or is it in the the results file (and thus ultimately the MP file)?
# * Is it ok for a MasterPlate_ file to have multiple sheets (e.g., readme tab- is only the first tab read in)?
# * What are the rules for pulling information from the MasterPlateFile to the !!Results_ (e.g., is it the column or the Header Name, etc that is searched? Particular cells in the DrugMedia file?).
# * Modifier, Conc are from DM sheet, and refer to the agar media arrays. OrfRep is from MasterPlate_ File. ‘Specifics’ (Last Column) is experiment specific and accommodate designs involving differences across the multi-well liquid arrays. ‘StrainBkGrd’ (now ‘Library location’) is in the 3rd column and reported after ‘Specifics’ at the last col of the ‘!!Results..’ file.
# * Do we have / could we make an indicator- work in progress or idle/complete with MP/DM and after gen-report. Now, we can check for the MPDMmat.mat file, or we can look in PrintResults, but would be nice to know without looking there.
# * File>>Load Experiment wasn’t working (no popup to redirect). Check this again.
easy() {
debug "Running: ${FUNCNAME[0]}"
EASY="/mnt/data/EASY/EasyDev2024/BU/EASY240430AppExported/EstartConsole.m"
#EASY="/mnt/data/EASY/EasyDev2024/BU/EASY240430AppExported/EstartConsole.m"
EASY="/mnt/data/EASY/EasyDev2024/BU/EASY240505AppExported/EASYConsole.m"
pushd "$SCAN_DIR" || return 1
@@ -447,6 +477,8 @@ easy() {
! ((YES)) && ask "Start EASY in MATLAB? This requires a GUI." && matlab -nosplash -r "$EASY"
# glob EASY output and make sure it exists
# currently this is just for informative purposes of how to glob some of the EASY output files
# The EASY output files need to be standardized
shopt -s nullglob
EASY_RESULTS_DIRS=( Results* )
shopt -u nullglob
@@ -508,7 +540,11 @@ module qhtcp
# * Do not double-click on the file from the directory.
# * When prompted, navigate to the ExpJobs folder and the PrintResults folder within the correct job folder.
# * Repeat this for every Exp# folder depending on how many experiments are being performed.
# * Note: Before doing this, it’s a good idea to compare the ref and non-ref CPP average and median values. If they are not approximately equal, then may be helpful to standardize Ref values to the measures of central tendency of the Non-refs, because the Ref CPPs are used for the z-scores, which should be centered around zero.
# * This script will copy the !!ResultsStd file (located in /PrintResults in the relevant job folder in /ExpJobs **rename this !!Results file before running front end; we normally use the ‘STD’ (not the ‘ELR’ file) chosen to the Exp# directory as can be seen in the “Current Folder” column in MATLAB, and it updates ‘StudiesDataArchive.txt’ file that resides in the /StudiesQHTCP folder. ‘StudiesDataArchive.txt’ is a log of file paths used for different studies, including timestamps.
#
# Do this to document the names, dates and paths of all the studies and experiment data used in each study. Note, one should only have a single ‘!!Results…’ file for each /Exp_ to prevent ambiguity and confusion. If you decide to use a new or different ‘!!Results…’ sheet from what was used in a previous “QHTCP Study”, remove the one not being used. NOTE: if you copy a ‘!!Results…’ file in by hand, it will not be recorded in the ‘StudiesDataArchive.txt’ file and so will not be documented for future reference. If you use the ExpFrontend.m utility it will append the new source for the raw !!Results… to the ‘StudiesDataArchive.txt’ file.
# As stated above, it is advantageous to think about the comparisons one wishes to make so as to order the experiments in a rational way as it relates to the presentation of plots. That is, which results from sheets and selected ‘interaction … .R’, user modified script, is used in /Exp1, Exp2, Exp3 and Exp4 as explained in the following section.
# TODO MUST CLEAN UP QHTCP TEMPLATE DIRECTORY
#
# Code/Directory Structure:
@@ -827,6 +863,7 @@ qhtcp() {
QHTCP_TEMPLATE_DIR="$SCRIPT_DIR/templates/qhtcp"
STUDY_TEMPLATE_DIR="$QHTCP_TEMPLATE_DIR/ExpTemplate"
OUTPUT_DIR="/mnt/data/StudiesQHTCP"
STUDIES_ARCHIVE="$OUTPUT_DIR/StudiesDataArchive.txt"
QHTCP_DIR="$OUTPUT_DIR/$PROJECT"
if [[ -d $QHTCP_DIR ]]; then
@@ -843,23 +880,22 @@ qhtcp() {
fi
# Print current studies
STUDY_INFO_FILE="$QHTCP_DIR/Code/StudyInfo.csv"
[[ -f $STUDY_INFO_FILE ]] &&
echo "Current studies from $STUDY_INFO_FILE" &&
cat "$STUDY_INFO_FILE"
STUDY_INFO="$QHTCP_DIR/Code/StudyInfo.csv"
[[ -f $STUDY_INFO ]] &&
echo "Current studies from $STUDY_INFO" &&
cat "$STUDY_INFO"
# Ask user edit STUDY_INFO_FILE
if ! ((YES)) && ask "Would you like to edit $STUDY_INFO_FILE to add or modify studies?"; then
# Ask user to edit STUDY_INFO
if ! ((YES)) && ask "Would you like to edit $STUDY_INFO to add or modify studies?"; then
cat <<-EOF
Give each experiment the labels you wish to be used for the plots and specific files.
Enter the desired Experiment names and order them in the way you want them to appear in the REMc heatmaps
EOF
nano "$STUDY_INFO_FILE"
nano "$STUDY_INFO"
fi
# Sets STUDIES_NUM
get_studies "$STUDY_INFO_FILE"
get_studies "$STUDY_INFO"
# Initialize missing dirs
for s in "${STUDIES_NUM[@]}"; do
@@ -872,32 +908,15 @@ qhtcp() {
fi
done
# MATLAB stuff
cat <<-EOF
ExpFrontend.m was made for recording into a spreadsheet
('StudiesDataArchive.txt') the date and files used (i.e., directory paths to the
!!Results files used as input for Z-interaction script) for each multi-experiment study.
mat_exp_frontend
Run the front end MATLAB programs in the correct order (e.g., run front end in "exp1"
folder to call the !!Results file for the experiment you named as exp1 in the StudyInfo.csv file)
The GTA and pairwise, TSHeatmaps, JoinInteractions and GTF Heatmap scripts use this table
to label results and heatmaps in a meaningful way for the user and others.
The BackgroundSD and ZscoreJoinSD fields will be filled automatically according to user
specifications, at a later step in the QHTCP study process.
Open MATLAB and in the application navigate to each specific /Exp folder,
call and execute ExpFrontend.m by clicking the play icon.
Use the "Open file" function from within Matlab.
Do not double-click on the file from the directory.
When prompted, navigate to the ExpJobs folder and the PrintResults folder within the correct job folder.
Repeat this for every Exp# folder depending on how many experiments are being performed.
The Exp# folder must correspond to the StudyInfo.csv created above.
EOF
if ! ((YES)) &&
ask "Start MATLAB to run ExpFrontend.m? This requires a GUI."; then
matlab -nosplash
fi
for s in "${STUDIES_NUM[@]}"; do
study_dir="$QHTCP_DIR/Exp$s"
# Z_InteractionTemplate.R
r_interactions "$study_dir" "!!Results"*
done
# Enter REMc directory to run the scripts there
pushd "$QHTCP_DIR/REMc" || return 1
@@ -961,6 +980,95 @@ gta() {
# * Functions you do not want to perform by default (submodules should be called modules)
# * Should not call cd or pushd (let module dictate)
submodule mat_exp_frontend
# @description Run the ExpFrontend.m program
mat_exp_frontend() {
debug "Running: ${FUNCNAME[0]}"
# MATLAB stuff
cat <<-EOF
ExpFrontend.m was made for recording into a spreadsheet
('StudiesDataArchive.txt') the date and files used (i.e., directory paths to the
!!Results files used as input for Z-interaction script) for each multi-experiment study.
Run the front end MATLAB programs in the correct order (e.g., run front end in "exp1"
folder to call the !!Results file for the experiment you named as exp1 in the StudyInfo.csv file)
The GTA and pairwise, TSHeatmaps, JoinInteractions and GTF Heatmap scripts use this table
to label results and heatmaps in a meaningful way for the user and others.
The BackgroundSD and ZscoreJoinSD fields will be filled automatically according to user
specifications, at a later step in the QHTCP study process.
Open MATLAB and in the application navigate to each specific /Exp folder,
call and execute ExpFrontend.m by clicking the play icon.
Use the "Open file" function from within Matlab.
Do not double-click on the file from the directory.
When prompted, navigate to the ExpJobs folder and the PrintResults folder within the correct job folder.
Repeat this for every Exp# folder depending on how many experiments are being performed.
The Exp# folder must correspond to the StudyInfo.csv created above.
EOF
if ! ((YES)) &&
ask "Start MATLAB to run ExpFrontend.m? This requires a GUI."; then
matlab -nosplash
fi
[[ -f $STUDIES_ARCHIVE ]] || (err "$STUDIES_ARCHIVE missing"; return 1)
}
submodule r_interactions
# @description Run the R interactions analysis
# TODO don't want to rename Z_InteractionTemplate.R because that will break logic, just edit in place instead
# Is this script interactive
# @arg $1 string The current working directory
r_interactions() {
debug "Running: ${FUNCNAME[0]}"
cat <<-EOF
In each /Exp# folder, rename the Z_InteractionTemplate.R script according to the experiment focus
Example: Interaction, Experimenter Initials, Experiment Focus --> ‘int_RM_2PE.R’
5. Open the renamed interaction script, and edit each one beginning at the ‘++BEGIN USER DATA SELECTION++’
This is designed so that the data of interest for each experiment is appropriately selected from the !!Results…txt file
The user can edit, step through, and test the R script without running through the whole routine by observing the resultant data table created in RStudio.
The Z_InteractionTemplate.R script has a collection of code lines that have been used for prior analyses (generally to select data from various !!Results…txt files), which may be commented out (if not relevant), reused as needed, and/or modified for a new study. These include lines associated with the removal of ‘dAmps’, specific concentrations, and items described in the ‘Specifics’ and ‘Media’, i.e., information specific to a particular experiment design. There are also code lines to replace gene names ‘OCT1/YKL134C’ /’MAY24/YPR153W’ and that get converted to date format in excel, by using only the ORF name and to remove data rows with ‘Blank’ listed; these lines of code convenient to reuse. Hopefully, these code lines can be used, commented out, or adapted to aid the user in modifying this section to the specific data requirements of the study. As a new user data filter code is developed for each ‘Study’ (and vetted), those lines can be added to the InteractionTemplate230119.R code in the /StudyTemplate folders to aid in future studies.
6. Open a terminal, navigate to each /Exp# folder, and execute the (customized) ‘Z_InteractionTemplate_…” script by using the command line below:
Rscript RenamedInteractionTemplate.R \!\!Results… .txt
**need to change wording to choose SD of Delta_Background to exclude Data from analysis.
[1] "Be sure to enter Background noise filter standard deviation i.e., 3 or 5 per Sean"
Enter a Standard Deviation value to noise filter >>
[1] Enter Standard deviation value for removing data for cultures due to high background (e.g., contaminated cultures). Generally set this very high (e.g., ‘20’) on the first run in order NOT to remove data, e.g. ‘20’. Review QC data and inspect raw image data to decide if it is desirable to remove data, and then rerun analysis.
Enter a Background SD threshold for EXCLUDING culture data from further analysis:
The script will request for the user to input a ‘Background Standard Deviation Value’. This Background value removes data where there is high pixel intensity in the background regions of a spot culture (i.e., suspected contamination). 5 is a minimum recommended value, because lower values result in more data being removed, and often times this is undesirable if contamination occurs late after the carrying capacity of the yeast culture is reached. This is most often “trial and error”, meaning there is a ‘Frequency_Delta_Background.pdf’ report in the /Exp_/ZScores/QC/ folder to evaluate whether the chosen value was suitable (and if not the analysis can simply be rerun with a more optimal choice). In general, err on the high side, with BSD of 10 or 12…. One can also use EZview to examine the raw images and individual cultures potentially included/excluded as a consequence of the selected value. Background values are reported in the results sheet and so could also be analyzed there..
(For new terminal users, directory navigation tips are described below)
To navigate to the directory one can use the directory GUI (in X2Go, use the GUI to navigate to desired operating directory and then from the ‘File’ menu, choose “Open in Terminal’)
Alternatively, navigate there through the terminal window: ‘pwd’ “prints the current working directory”, ‘ls’ “lists” the subfolders in the current directory. ‘cd’’ followed by the name of the ‘subdirectory’ will move down into it. “cd .. “ changes to the parent directory
The tab key can be used to autofill unique characters after typing the initial letters of a folder or file you wish to call.
The template structure above assists the user with organization and management of Q-HTCP files and provides a uniform directory structure to streamline reference across different users and experiments.
Since we are systematically comparing perturbations, most Q-HTCP studies will consist of either 2 or 4 experiment subfolders.
The Zscores files are used for subsequent analyses, including REMc, GTA and Term Specific Heatmaps. These further analyses are described below and can be completed in any order and/or concurrently from separate terminals.
**Annotate Files produced and comment out code that produces files that are obsolete or clutter.
EOF
script="$1/Z_InteractionTemplate.R"
debug "$RSCRIPT $script"
"$RSCRIPT" "$script"
# 1. Path to input file
# 2. /output/ directory
# 3. Path to StudyInfo.csv
# 4. Standard deviation value
}
submodule r_join_interact
# @description JoinInteractExps3dev.R creates REMcRdy_lm_only.csv and Shift_only.csv
r_join_interact() {

246
workflow/templates/easy/DMPexcel2mat.m Executable file
View File

@@ -0,0 +1,246 @@
%% CALLED BY EASYconsole.m %%
w = pwd;
%{
cd ..
if exist('ExpJobs/')
cd('ExpJobs/');
else
pwd
end
%}
try
cd(ExpPath)
catch
cd(w)
end
pwd
numOfMPs=0;
%GUI input for selecting a MasterPlate Excel file
questdlg('\fontsize{20} Select Master Plate File','File Selection','OK', struct('Default','OK','Interpreter','tex'))
[Scanfiles, pathname]=uigetfile('*.*','MultiSelect','off');
if ispc
MPdir= fullfile(pathname,'\');
else
MPdir=fullfile(pathname,'/');
end
infile= Scanfiles(1,:);
cd(MPdir)
%fid=fopen(infile)%('exp23PrintTimes.xls'); % textread puts date and time sequentially into vector
if ispc
[num, txt, raw] = xlsread(infile); %,'Yor1HitsMPsetFinal');
fields= {txt(2,1:15)}; %or 1:17 for later but dont wish to exceed and cause error ? if used
else
clear MPtbl
opts = detectImportOptions(infile);
MPtbl = readtable(infile,opts);
MPtbl= readtable(infile);
fields= {opts.VariableNames}; %? if used anywhere although 'saved' to MPDMmat
MPcell= readcell(infile);
end
cd(w)
numb= 0;
clear MP;
try
if ispc
excLnNum=3;
while (isequal(txt{excLnNum,1},'###'))
numb=numb+1;
MP(numb).head = {raw(excLnNum,2:6)};
MP(numb).recNum = {raw((excLnNum+1):(excLnNum+384),1)};
MP(numb).orf = {raw((excLnNum+1):(excLnNum+384),2)};
MP(numb).strain = {raw((excLnNum+1):(excLnNum+384),3)};
MP(numb).genename= {raw((excLnNum+1):(excLnNum+384),12)};
MP(numb).drug= {raw((excLnNum+1):(excLnNum+384),8)};
MP(numb).media= {raw((excLnNum+1):(excLnNum+384),7)};
if size(raw,2)>15
MP(numb).orfRep= {raw((excLnNum+1):(excLnNum+384),16)}; %added 12_1005 to specify replicates Orfs in MP
MP(numb).specifics= {raw((excLnNum+1):(excLnNum+384),17)}; %added 12_1008 to specify replicates Specific details in MP
else
MP(numb).orfRep= ' ';
MP(numb).specifics= ' ';
end
%{
if size(raw,2)>17 ; Future MP field
MP(numb).specifics2= {raw((excLnNum+1):(excLnNum+384),18)}; %added 12_1008 to specify strain Bkground in MP
else
MP(numb).specifics2= ' ';
end
%}
excLnNum=excLnNum+385;
msg=strcat('NumberOfMP = ',num2str(numb), ' lastLineNo. = ',num2str(excLnNum));
end % end if ispc
else %if not ispc
excLnNum=1;
while (isequal(MPcell{(excLnNum+2),1},'###'))
numb=numb+1;
MP(numb).head = {MPtbl(excLnNum,2:6)};
MP(numb).head{1}= table2cell(MP(numb).head{1});
MP(numb).recNum = {MPtbl((excLnNum+1):(excLnNum+384),1)};
MP(numb).recNum{1}= table2cell(MP(numb).recNum{1});
MP(numb).orf = {MPtbl((excLnNum+1):(excLnNum+384),2)};
MP(numb).orf{1}= table2cell(MP(numb).orf{1});
MP(numb).strain = {MPtbl((excLnNum+1):(excLnNum+384),3)};
MP(numb).strain{1}= table2cell(MP(numb).strain{1});
MP(numb).genename= {MPtbl((excLnNum+1):(excLnNum+384),12)};
MP(numb).genename{1}= table2cell(MP(numb).genename{1});
MP(numb).media= {MPtbl((excLnNum+1):(excLnNum+384),7)};
MP(numb).media{1}= table2cell(MP(numb).media{1});
if size(MPtbl,2)>15
MP(numb).orfRep= {MPtbl((excLnNum+1):(excLnNum+384),16)}; %added 12_1005 to specify replicates Orfs in MP
MP(numb).orfRep{1}= table2cell(MP(numb).orfRep{1});
MP(numb).specifics= {MPtbl((excLnNum+1):(excLnNum+384),17)}; %added 12_1008 to specify replicates Specific details in MP
MP(numb).specifics{1}= table2cell(MP(numb).specifics{1});
else
MP(numb).orfRep= ' ';
MP(numb).specifics= ' ';
end
excLnNum=excLnNum+385;
msg=strcat('NumberOfMP = ',num2str(numb), 'lastLineNo. = ',num2str(excLnNum))
end
end %end of if ispc for MP while loop choice PC or Linux-other (ln~48)
catch ME
h = msgbox(msg,'Check Number of Master Plates and Excel Lines')
uiwait(h);
end %end for try MP excel sheet input
%*********************************************************************
%DMupload
%Drug and Media Plate setup Upload from Excel
%scan().plate().LocInd().gene
cd(MPdir);
excLnNum=1;
%w=pwd
%cd('D:\EASY\Experiments\'); %cd(ExpPath); %
numOfDrugs=0;
numOfMedias=0;
%GUI input for selecting a MasterPlate Excel file
questdlg('\fontsize{20} Select DrugMedia File','File Selection','OK', struct('Default','OK','Interpreter','tex'));
[Scanfiles, pathname]=uigetfile('*.*', 'MultiSelect','off');
if ispc
DMdir= fullfile(pathname,'\');
else
DMdir=fullfile(pathname,'/');
end
clear infile;
infile= Scanfiles(1,:);
cd(DMdir)
%fid=fopen(infile)%('exp23PrintTimes.xls'); % textread puts date and time sequentially into vector
if ispc
[num, txt, raw] = xlsread(infile); %,'Yor1HitsMPsetFinal');
fields= {txt(2,1:5)};
Linked= num(1,1);
else
opts = detectImportOptions(infile);
DMtbl= readtable(infile,opts);
fields= opts.VariableOptions;
Linked= DMtbl{1,1};
DMcell= readcell(infile);
end
cd(w)
numb=0;
%fields= {txt(2,1:5)};
%Linked= num(1,1);
if isequal(Linked,1) %Drugs and Media are linked 1 to 1; else they are combinatorial
clear DM;
%try
excLnNum=2;
if ispc
while (~isequal(txt{excLnNum,2},'###'))
numb=numb+1;
DM.drug(numb) = {raw(excLnNum,2)};
DM.conc(numb) = {raw(excLnNum,3)};
DM.media(numb) = {raw(excLnNum,4)};
DM.mod1(numb) = {raw(excLnNum,5)};
DM.conc1(numb) = {raw(excLnNum,6)};
DM.mod2(numb) = {raw(excLnNum,7)};
DM.conc2(numb) = {raw(excLnNum,8)};
excLnNum=excLnNum+1;
msg=strcat('NumberOf1:1DrugMediaPlates = ',num2str(numb), ' lastLineNo. = ',num2str(excLnNum))
end
else
clear DM
excLnNum=1;
while (~isequal(DMcell{excLnNum+1,2},'###'))
numb=numb+1;
DM.drug(numb) = {DMtbl(excLnNum,2)};
DM.drug(numb)= table2cell(DM.drug{numb});
DM.conc(numb) = {DMtbl(excLnNum,3)};
DM.conc(numb)= table2cell(DM.conc{numb});
DM.media(numb) = {DMtbl(excLnNum,4)};
DM.media(numb)= table2cell(DM.media{numb});
DM.mod1(numb) = {DMtbl(excLnNum,5)};
DM.mod1(numb)= table2cell(DM.mod1{numb});
DM.conc1(numb) = {DMtbl(excLnNum,6)};
DM.conc1(numb)= table2cell(DM.conc1{numb});
DM.mod2(numb) = {DMtbl(excLnNum,7)};
DM.mod2(numb)= table2cell(DM.mod2{numb});
DM.conc2(numb) = {DMtbl(excLnNum,8)};
DM.conc2(numb)= table2cell(DM.conc2{numb});
excLnNum=excLnNum+1;
msg=strcat('NumberOf1:1DrugMediaPlates = ',num2str(numb), ' lastLineNo. = ',num2str(excLnNum))
end
end
end
%Legacy contengency -Not ever used!!
if isequal(Linked,0) %0 indicates Drugs and Media are combinatorial
clear DM;
excLnNum=2;
drgCnt=0;
medCnt=0;
if ispc
while (~isequal(txt{excLnNum,2},'###'))
drgCnt=drgCnt+1;
DM.drug(drgCnt) = {raw(excLnNum,2)};
DM.conc(drgCnt) = {raw(excLnNum,3)};
excLnNum=excLnNum+1;
end
while (~isequal(txt{excLnNum,4},'###'))
medCnt=medCnt+1;
DM.media(medCnt) = {raw(excLnNum,4)};
excLnNum=excLnNum+1;
end
else %else if not PC (Then linux or other)
excLnNum=1;
while (~isequal(DMcell{excLnNum+1,2},'###'))
drgCnt=drgCnt+1;
DM.drug(drgCnt) = {DMtbl(excLnNum,2)};
DM.conc(drgCnt) = {DMtbl(excLnNum,3)};
excLnNum=excLnNum+1;
end
while (~isequal(DMcel{excLnNum+1,4},'###'))
medCnt=medCnt+1;
DM.media(medCnt) = {DMtbl(excLnNum,4)};
excLnNum=excLnNum+1;
end
end
msg=strcat('NumberOfDrugs = ',num2str(drgCnt), ' NumberOfMedias = ',num2str(medCnt) )
end
save (fullfile(MPdir,'MPDMmat'), 'fields','MP','DM','Linked');
cd(w)
msgbox(['Drug-Media-MasterPlate Annotation File Generation Complete'])

727
workflow/templates/easy/DgenResults.m Executable file
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@@ -0,0 +1,727 @@
%% CALLED BY EASYconsole.m %%
%to 'Fotos' from 'PTmaps'
%Console globals*******
global ExpPath
global resDir
global ExpOutmat
global ImParMat
w=pwd;
ln=1;
%******Version compatability fixes*******assoc'd with diff and solve v11a='7.12.0.635 (R2011a)';
if verLessThan('matlab','8.3') %original work 23_0227 updated 23_0525 (8.4 changed to 8.3)
fd4=diff(sym('K / (1 + exp(-r* (t - l )))'),4);
sols= solve(fd4);
else %accomodate new matlab changes after 2014a fix 2nd update 23_0227
syms t K r l;
fd4= diff(K / (1 + exp(-r* (t - l ))),t,4);
sols= solve(fd4);
tmpswap= sols(1);
sols(1)= sols(3);
sols(3)= tmpswap;
end
%MPnum=ImParMat(1);
%opt = questdlg('Print Results Only (RES), DB Only (DB), or Both','Results Printout Options','Res','DB','Both','Both');
opt='Res';
if ~exist('ImParMat','var') || isempty(ImParMat)
load ImParameters
end
destPerMP=ImParMat(2);
load (ExpOutmat);
load (fullfile(ExpPath,'MasterPlateFiles','MPDMmat.mat'))
numOfDrgs= length(DM.drug);
numOfMeds= length(DM.media);
destPerMP=numOfDrgs;
%Determine the longest set of intensity(tPts) for the Experiment Data Set
maxNumIntens=0;
for n=1:size(scan,2)
for m=1:size(scan(n).plate,2)
maxNumIntens= max(maxNumIntens,size(scan(n).plate(m).intens,2));
end
end
if length(ExpPath)== max(strfind(ExpPath,'\'))
localExpPath=ExpPath(1:end-1);
else
localExpPath=ExpPath;
end
if ispc %Linux accommodation
expNm=localExpPath(max(strfind(localExpPath,'\'))+1:end);
else
if isunix,expNm=localExpPath(max(strfind(localExpPath,'/'))+1:end);end
if ismac,expNm=localExpPath(max(strfind(localExpPath,'/'))+1:end);end
end
if ispc
drivePos=min(strfind(localExpPath,'\'));
else
drivePos= min(strfind(localExpPath,'/'));
end
drive= localExpPath(1:(drivePos-1));
DBupload=fullfile(drive,'EZdbFiles','DBupLOADfiles');
%DBupload=['G:\EZdbFiles\DBupLOADfiles']
%resultsFilename= strcat(resDir,'\PrintResults\!!Results_Output.txt') %'\PrintResults\zDevelCFitOutIndxSelectedRawDatTimesDrugMedia.txt'
%DBfilename= strcat(resDir,'\PrintResults\!!Dbase_Output.txt') % Print !Dbase file in PrintResults dir
%resultsFilename= strcat(resDir,'\PrintResults\!!Results_',expNm,'.txt')
%DBfilename= strcat(resDir,'\PrintResults\!!Dbase_',expNm,'.txt')
%Added to allow backward compatability************************************
%Test for CFoutStd as indication of 2018version with r_refined fit code;If
%earlier version with only a standard composite fite, Print results to
%!!ResultsStd_...txt only
%***********************
try
scan(1).plate(1).CFoutStd(1,1);
resultsFilename= fullfile(resDir,'PrintResults', strcat('!!ResultsELr_',expNm,'.txt'));
DBfilename= fullfile(resDir,'PrintResults', strcat('!!DbaseELr_',expNm,'.txt'));
catch
resultsFilename= fullfile(resDir,'PrintResults', strcat('!!ResultsStd_',expNm,'.txt'));
DBfilename= fullfile(resDir,'PrintResults', strcat('!!DbaseStd_',expNm,'.txt'));
end
%**************************************************************************
if isequal(opt,'Res')||isequal(opt,'Both'),fid = fopen(resultsFilename,'w');end
if isequal(opt,'DB')||isequal(opt,'Both'),fid2 = fopen(DBfilename,'w');end %121012 Combo
if isequal(opt,'Res')||isequal(opt,'Both') %print Results
fprintf(fid,'%d\t',ln); %Results header
fprintf(fid,'%s\t\n',localExpPath);
ln=ln+1;
fprintf(fid,'%d\t',ln);
end
mpCnt=0;
totPlCnt=0;
drgCnt=0;
medCnt=0;
%load(fullfile(resDir,'PTmats','Nbdg')) %Convolute scan array data into plates
try
load(fullfile(resDir,'Fotos','Nbdg')) %Convolute scan array data into plates
catch
load(fullfile(resDir,'PTmats','Nbdg')) %Convolute scan array data into plates
end
for s=1:size(scan,2)
%Convolute scan array data into plates DconB for DBcombo
clear Diag
try
Diag(:,:,:,1)= sbdg{s}(1:1:24,16:-1:1,:);
catch
sbdg{s};
end
%*****************************************************
for p=1:size((scan(s).plate),2)
totPlCnt=totPlCnt+1;
if destPerMP>1 &&rem(totPlCnt,destPerMP)==1, mpCnt=mpCnt+1; end
if destPerMP==1,mpCnt=mpCnt+1; end
pertCnt= rem(totPlCnt,destPerMP);
if pertCnt==0, pertCnt= destPerMP;end
pert= strcat('Perturb_',num2str(pertCnt));
s
p
clear outCmat
outCmat=scan(s).plate(p).CFout;
%Print Time Point HEADER for each plate for newly added intensity data
if isequal(opt,'Res')||isequal(opt,'Both')
fprintf(fid, '\n');
ln=ln+1;
fprintf(fid,'%d\t',ln);
fprintf(fid,'Scan\tPlate\tRow\tCol\t');
try
asd=cell2mat(scan(s).plate(1).CFparameters(1));
aucEndPt= strcat('AUC',num2str(asd(9)));
catch
asd=cell2mat(scan(s).plate(1).CFparameters{1,1}(1,384));
aucEndPt= strcat('AUC',num2str(asd(9)));
end
fprintf(fid, 'Num.\tDiagnostics\tDrug\tConc\tMedia\tModifier1\tConc1\tModifier2\tConc2\tORF\tGene');
fprintf(fid, '\t %s',aucEndPt);
fprintf(fid, '\triseTm\tK\tr\tl\tR-squared\tK-lower\tK-upper\tr-lower\tr-upper\tl-lower\tl-upper\tArea\tLastInten\tSplineMaxRateTm\tLastFitTm\t1stFitTm\tMedianBase\tFitBase\tMinTm\tThreshTm');
if size(outCmat,2)==27
fprintf(fid, '\ttc11Cut\ttc12Cut\ttc21Cut\ttc22Cut'); %'\tEarly1\tEarly2\tLate1\tLate2'); 17_0629 MinBaseIntens update for MedianBase label
end
fprintf(fid, '\tTotFitPts\tPostThreshFitPts\t1stBackgrd\tLstBackgrd\t1stMeanTotBackgrd\tLstMeanTotBackgrd');
end
clear outTseries
outTseries=[];
outTseries=scan(s).plate(p).tSeries;
TseriesSize= size(outTseries,1);
%***************************************************************
%clear outCmat
%outCmat=scan(s).plate(p).CFout;
clear outIntens
outIntens=[];
RawIntens=[];
RawIntens=scan(s).plate(p).intens;
RawIntensSize= size(RawIntens,2)
clear Ag; %Ag is Growth Area
Ag=scan(s).plate(p).Ag;
AgSize= size(Ag);
%***************************************
dataLength= min(TseriesSize,RawIntensSize);
%for j=1:length(outTseries)%(size(outTseries,2)
if isequal(opt,'Res')||isequal(opt,'Both')
for j=1:dataLength
fprintf(fid, '\t%.5f', outTseries(j));
end
end
%numBlkColTm=(maxNumIntens - size(outTseries,1));
numBlkCol=(maxNumIntens - dataLength); %size(outTseries,1));
%for nn=1:numBlkColTm %extend to col beyond longest rawDataSet
if isequal(opt,'Res')||isequal(opt,'Both')
for nn=1:numBlkCol %extend to col beyond longest rawDataSet
fprintf(fid, '\t');
end
fprintf(fid,'\tOrfRep');
fprintf(fid,'\tSpecifics');
fprintf(fid,'\tStrainBkGrd');
fprintf(fid, '\n');
ln=ln+1;
fprintf(fid,'%d\t',ln);
end
%*****************************************Begin Data Section
n=0;
for r=1:16
for c=1:24
n=n+1;
clear selcode;
Kval=outCmat(n,3);
rSq=outCmat(n,6);
lval=outCmat(n,5);
if Kval>160, selcode='K_Hi'; else selcode=' ';end
if Kval<40, selcode=strcat(selcode,' K_Lo'); end %12_1030
if rSq<.97 && rSq>0, selcode=strcat(selcode,' rSqLo'); end
if lval>(0.85*(max(outTseries))), selcode=strcat(selcode,' late');end
if isnan(outCmat(n,7))||isnan(outCmat(n,8))||isnan(outCmat(n,9))...
||isnan(outCmat(n,10))||isnan(outCmat(n,11))...
||isnan(outCmat(n,12)), selcode=strcat(selcode,' NaN');
end
%*************RiseTime Calculation*****************************************
K= (outCmat(n,3));
R= (outCmat(n,4));
L= (outCmat(n,5));
if R>0 && L>0 && K>0
rr=R; ll=L;
tc1= eval(sols(2));
tc2= eval(sols(3));
LL= eval(sols(1));
riseTm= LL-tc1;
else
riseTm=0;
end
%*************************************************************************
if Ag(n)< .30*(scan(s).Awindow),selcode=strcat(selcode,' smArea'); end %12_1030
if outCmat(n,3)==0,selcode=strcat('0 ',selcode); end
orf=cell2mat(MP(mpCnt).orf{1}(n));
gene=cell2mat(MP(mpCnt).genename{1}(n));
orfRep=cell2mat(MP(mpCnt).orfRep{1}(n));
specifics=cell2mat(MP(mpCnt).specifics{1}(n));
strain=cell2mat(MP(mpCnt).strain{1}(n));
drug= char(DM.drug{pertCnt});
conc= char(DM.conc{pertCnt});
media= char(DM.media{pertCnt});
try
mod1= char(DM.mod1{pertCnt});
conc1= char(DM.conc1{pertCnt});
catch
mod1= ' ';
conc1= ' ';
end
try
mod2= char(DM.mod2{pertCnt});
conc2= char(DM.conc2{pertCnt});
catch
mod2= ' ';
conc2= ' ';
end
if ~isempty(outCmat)
if isequal(opt,'Res')||isequal(opt,'Both')
fprintf(fid,'%d\t %d\t %d\t %d\t %d\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t',s,p,r,c,n,selcode,drug,conc,media,mod1,conc1,mod2,conc2,orf,gene);
fprintf(fid, '%.5f\t %.5f\t %.5f\t %.5f\t %.5f\t %.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f',...
outCmat(n,1),riseTm,outCmat(n,3),outCmat(n,4),...
outCmat(n,5),outCmat(n,6),outCmat(n,7),outCmat(n,8),...
outCmat(n,9),outCmat(n,10),outCmat(n,11),outCmat(n,12),...
outCmat(n,13),outCmat(n,14),outCmat(n,15),outCmat(n,16));
fprintf(fid, '\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f',...
outCmat(n,17),outCmat(n,18),outCmat(n,19),...
outCmat(n,20),outCmat(n,21));
%failPt= [s n r c]
%Added for data cut times used in 'r'optomized method 06/14/2018
if size(outCmat,2)==27
fprintf(fid, '\t%.5f\t%.5f\t%.5f\t%.5f',...
outCmat(n,24),outCmat(n,25),outCmat(n,26),outCmat(n,27));
end
fprintf(fid, '\t%d\t%d\t%d\t%d\t%d\t%d',...
outCmat(n,22),outCmat(n,23),Diag(c,r,1,p),Diag(c,r,2,p),Diag(c,r,3,p),Diag(c,r,4,p)); %,Diag(r,c,3,p),Diag(r,c,4,p));
end %Results print
%DBfile*******************************************
%riseTm calc*****
if isequal(opt,'DB')||isequal(opt,'Both')
dbRsq= 0;dbKup= 0; dbKlo= 0; dbrup= 0; dbrlo= 0; dbLlo= 0; dbLup= 0;
if isnumeric(outCmat(n,6)), dbRsq= outCmat(n,6);end
if isnumeric(outCmat(n,7)), dbKup= outCmat(n,7);end
if isnumeric(outCmat(n,8)), dbKlo= outCmat(n,8);end
if isnumeric(outCmat(n,9)), dbrup= outCmat(n,9);end
if isnumeric(outCmat(n,10)), dbrlo= outCmat(n,10);end
if isnumeric(outCmat(n,11)), dbLlo= outCmat(n,11);end
if isnumeric(outCmat(n,12)), dbLup= outCmat(n,12);end
end
%****************
if isequal(opt,'DB')||isequal(opt,'Both')
fprintf(fid2,'%s\t %d\t %d\t %d\t %d\t %d\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t',expNm,s,p,r,c,n,selcode,drug,conc,media,mod1,conc1,mod2,conc2,orf,gene);
fprintf(fid2, '%.5f\t %.5f\t %.5f\t %.5f\t %.5f\t %.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f',...
outCmat(n,1),riseTm,outCmat(n,3),outCmat(n,4),...
outCmat(n,5),dbRsq,dbKup,dbKlo,...
dbrup,dbrlo,dbLlo,dbLup); %\t%.5f\t%.5f\t%.5f\t%.5f
%... outCmat(n,13),outCmat(n,14),outCmat(n,15),outCmat(n,16));
end
%*****DB analysis data end************************************************
%Add Intensities series to end of curve fit data
outIntens=[];
outIntens=zeros(384,dataLength);
intensBlob='';
tmBlob ='';
for j=1:dataLength %size(RawIntens,2) %size(outTseries,1)
if Ag(n)==0,Ag(n)=scan(s).Awindow;end
outIntens(n,j)= RawIntens(n,j)/Ag(n);
if isequal(opt,'Res')||isequal(opt,'Both')
fprintf(fid, '\t%.5f', outIntens(n,j)); % Results print Intens
end
if isequal(opt,'DB')||isequal(opt,'Both')
if j<dataLength
intensBlob= strcat(intensBlob,num2str(outIntens(n,j)),';');
else
intensBlob= strcat(intensBlob,num2str(outIntens(n,j)));
end
if outTseries(j)<.0001,outTseries(j)=0;end
if j<dataLength
tmBlob= strcat(tmBlob,num2str(outTseries(j)),';');
else
tmBlob= strcat(tmBlob,num2str(outTseries(j)));
end
end %if DB
end %j
%***************************
% Results fprint***********
if isequal(opt,'Res')||isequal(opt,'Both')
for nn=1:numBlkCol %extend to col beyond longest rawDataSet
fprintf(fid, '\t');
end
%-----------------------------------------------
% UPDATE 14_0626 to writein ' ' if personnel fail to in their
% Masterplate sheet
if ~isnan(orfRep)
fprintf(fid, '\t%s', orfRep); %print OrfRep
else
fprintf(fid, '\t%s', ' ');
end
if ~isnan(specifics)
fprintf(fid, '\t%s', specifics);
else
fprintf(fid, '\t%s', ' ');
end
if ~isnan(strain)
fprintf(fid, '\t%s', strain);
else
fprintf(fid, '\t%s', ' ');
end
%-----------------------------------------------
%****************************
fprintf(fid, '\n');
ln=ln+1;
fprintf(fid,'%d\t',ln);
end
%****************************
%DB Raw Intensities and Timepoints
if isequal(opt,'DB')||isequal(opt,'Both')
fprintf(fid2, '\t%s\t%s',intensBlob,tmBlob );
%-------------------------------
% UPDATE 14_0626 to writein ' ' if personnel fail to in their
% Masterplate sheet
if ~isnan(orfRep)
fprintf(fid2, '\t%s',orfRep );
else
fprintf(fid2, '\t%s', ' ');
end
if ~isnan(specifics)
fprintf(fid2, '\t%s',specifics );
else
fprintf(fid2, '\t%s', ' ');
end
if ~isnan(strain)
fprintf(fid2, '\t%s',strain );
else
fprintf(fid2, '\t%s', ' ');
end
%---------------------------------
fprintf(fid2, '\n');
end %DB print
end %if ~isempty(outCmat)
end %c
end %r
end %p
end %s
if isequal(opt,'Res')||isequal(opt,'Both')
fclose(fid);
end
if isequal(opt,'DB')||isequal(opt,'Both')
fclose(fid2);
try
copyfile(DBfilename,DBupload)
catch ME
rep = getReport(ME, 'basic');
rep=strcat('Failed copyfile to ',DBupload,' -', rep);
errordlg(rep)
end
end %if DB
ln;
cd(w)
%***********************************************************************
%BEGIN PRINT RESULTS ROUTINE FOR STANDARD METHOD
%***********************************************************************
try
scan(1).plate(1).CFoutStd(1,1) %Test for 2018 r_refined version
ln=1;
resultsFilename= fullfile(resDir,'PrintResults', strcat('!!ResultsStd_',expNm,'.txt'));
DBfilename= fullfile(resDir,'PrintResults', strcat('!!DbaseStd_',expNm,'.txt'));
if isequal(opt,'Res')||isequal(opt,'Both'),fid = fopen(resultsFilename,'w');end
if isequal(opt,'DB')||isequal(opt,'Both'),fid2 = fopen(DBfilename,'w');end %121012 Combo
if isequal(opt,'Res')||isequal(opt,'Both') %print Results
fprintf(fid,'%d\t',ln); %Results header
fprintf(fid,'%s\t\n',localExpPath);
ln=ln+1;
fprintf(fid,'%d\t',ln);
end
mpCnt=0;
totPlCnt=0;
drgCnt=0;
medCnt=0;
for s=1:size(scan,2)
%Convolute scan array data into plates DconB for DBcombo
clear Diag
try
Diag(:,:,:,1)= sbdg{s}(1:1:24,16:-1:1,:);
catch
sbdg{s};
end
%*****************************************************
for p=1:size((scan(s).plate),2)
totPlCnt=totPlCnt+1;
if destPerMP>1 &&rem(totPlCnt,destPerMP)==1, mpCnt=mpCnt+1; end
if destPerMP==1,mpCnt=mpCnt+1; end
pertCnt= rem(totPlCnt,destPerMP);
if pertCnt==0, pertCnt= destPerMP;end
pert= strcat('Perturb_',num2str(pertCnt));
s
%Print Time Point HEADER for each plate for newly added intensity data
if isequal(opt,'Res')||isequal(opt,'Both')
fprintf(fid, '\n');
ln=ln+1;
fprintf(fid,'%d\t',ln);
fprintf(fid,'Scan\tPlate\tRow\tCol\t');
try
asd=cell2mat(scan(s).plate(1).CFparameters(1));
aucEndPt= strcat('AUC',num2str(asd(9)));
catch
asd=cell2mat(scan(s).plate(1).CFparameters{1,1}(1,384));
aucEndPt= strcat('AUC',num2str(asd(9)));
end
fprintf(fid, 'Num.\tDiagnostics\tDrug\tConc\tMedia\tModifier1\tConc1\tModifier2\tConc2\tORF\tGene')
fprintf(fid, '\t %s',aucEndPt)
fprintf(fid, '\triseTm\tK\tr\tl\tR-squared\tK-lower\tK-upper\tr-lower\tr-upper\tl-lower\tl-upper\tArea\tLastInten\tSplineMaxRateTm\tLastFitTm\t1stFitTm\tMedianBase\tFitBase\tMinTm\tThreshTm\tTotFitPts\tPostThreshFitPts\t1stBackgrd\tLstBackgrd\t1stMeanTotBackgrd\tLstMeanTotBackgrd'); %17_0629 MinBaseIntens update for MedianBase label
end
clear outTseries
outTseries=[];
outTseries=scan(s).plate(p).tSeries;
TseriesSize= size(outTseries,1);
%***************************************************************
clear outCmat
outCmat=scan(s).plate(p).CFoutStd;
clear outIntens
outIntens=[];
RawIntens=[];
RawIntens=scan(s).plate(p).intens;
RawIntensSize= size(RawIntens,2)
clear Ag; %Ag is Growth Area
Ag=scan(s).plate(p).Ag;
AgSize= size(Ag);
%***************************************
dataLength= min(TseriesSize,RawIntensSize);
if isequal(opt,'Res')||isequal(opt,'Both')
for j=1:dataLength
fprintf(fid, '\t%.5f', outTseries(j));
end
end
numBlkCol=(maxNumIntens - dataLength); %size(outTseries,1));
if isequal(opt,'Res')||isequal(opt,'Both')
for nn=1:numBlkCol %extend to col beyond longest rawDataSet
fprintf(fid, '\t');
end
fprintf(fid,'\tOrfRep');
fprintf(fid,'\tSpecifics');
fprintf(fid,'\tStrainBkGrd');
fprintf(fid, '\n');
ln=ln+1;
fprintf(fid,'%d\t',ln);
end
%*****************************************Begin Data Section
n=0;
for r=1:16
for c=1:24
n=n+1;
clear selcode;
Kval=outCmat(n,3);
rSq=outCmat(n,6);
lval=outCmat(n,5);
if Kval>160, selcode='K_Hi'; else selcode=' ';end
if Kval<40, selcode=strcat(selcode,' K_Lo'); end %12_1030
if rSq<.97 && rSq>0, selcode=strcat(selcode,' rSqLo'); end
if lval>(0.85*(max(outTseries))), selcode=strcat(selcode,' late');end
if isnan(outCmat(n,7))||isnan(outCmat(n,8))||isnan(outCmat(n,9))...
||isnan(outCmat(n,10))||isnan(outCmat(n,11))...
||isnan(outCmat(n,12)), selcode=strcat(selcode,' NaN');
end
%*************RiseTime Calculation*****************************************
K= (outCmat(n,3));
R= (outCmat(n,4));
L= (outCmat(n,5));
if R>0 && L>0 && K>0
rr=R; ll=L;
tc1= eval(sols(2));
tc2= eval(sols(3));
LL= eval(sols(1));
riseTm= LL-tc1;
else
riseTm=0;
end
%*************************************************************************
if Ag(n)< .30*(scan(s).Awindow),selcode=strcat(selcode,' smArea'); end %12_1030
if outCmat(n,3)==0,selcode=strcat('0 ',selcode); end
orf=cell2mat(MP(mpCnt).orf{1}(n));
gene=cell2mat(MP(mpCnt).genename{1}(n));
orfRep=cell2mat(MP(mpCnt).orfRep{1}(n));
specifics=cell2mat(MP(mpCnt).specifics{1}(n));
strain=cell2mat(MP(mpCnt).strain{1}(n));
drug= char(DM.drug{pertCnt});
conc= char(DM.conc{pertCnt});
media= char(DM.media{pertCnt});
try
mod1= char(DM.mod1{pertCnt});
conc1= char(DM.conc1{pertCnt});
catch
mod1= ' ';
conc1= ' ';
end
try
mod2= char(DM.mod2{pertCnt});
conc2= char(DM.conc2{pertCnt});
catch
mod2= ' ';
conc2= ' ';
end
if ~isempty(outCmat)
if isequal(opt,'Res')||isequal(opt,'Both')
fprintf(fid,'%d\t %d\t %d\t %d\t %d\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t',s,p,r,c,n,selcode,drug,conc,media,mod1,conc1,mod2,conc2,orf,gene);
fprintf(fid, '%.5f\t %.5f\t %.5f\t %.5f\t %.5f\t %.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f',...
outCmat(n,1),riseTm,outCmat(n,3),outCmat(n,4),...
outCmat(n,5),outCmat(n,6),outCmat(n,7),outCmat(n,8),...
outCmat(n,9),outCmat(n,10),outCmat(n,11),outCmat(n,12),...
outCmat(n,13),outCmat(n,14),outCmat(n,15),outCmat(n,16));
fprintf(fid, '\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%d\t%d',...
outCmat(n,17),outCmat(n,18),outCmat(n,19),...
outCmat(n,20),outCmat(n,21),outCmat(n,22),outCmat(n,23));
fprintf(fid, '\t%d\t%d\t%d\t%d',...
Diag(c,r,1,p),Diag(c,r,2,p),Diag(c,r,3,p),Diag(c,r,4,p)); %,Diag(r,c,3,p),Diag(r,c,4,p));
end %Results print
%DBfile*******************************************
%riseTm calc*****
if isequal(opt,'DB')||isequal(opt,'Both')
dbRsq= 0;dbKup= 0; dbKlo= 0; dbrup= 0; dbrlo= 0; dbLlo= 0; dbLup= 0;
if isnumeric(outCmat(n,6)), dbRsq= outCmat(n,6);end
if isnumeric(outCmat(n,7)), dbKup= outCmat(n,7);end
if isnumeric(outCmat(n,8)), dbKlo= outCmat(n,8);end
if isnumeric(outCmat(n,9)), dbrup= outCmat(n,9);end
if isnumeric(outCmat(n,10)), dbrlo= outCmat(n,10);end
if isnumeric(outCmat(n,11)), dbLlo= outCmat(n,11);end
if isnumeric(outCmat(n,12)), dbLup= outCmat(n,12);end
end
%****************
if isequal(opt,'DB')||isequal(opt,'Both')
fprintf(fid2,'%s\t %d\t %d\t %d\t %d\t %d\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t',expNm,s,p,r,c,n,selcode,drug,conc,media,mod1,conc1,mod2,conc2,orf,gene);
fprintf(fid2, '%.5f\t %.5f\t %.5f\t %.5f\t %.5f\t %.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f',...
outCmat(n,1),riseTm,outCmat(n,3),outCmat(n,4),...
outCmat(n,5),dbRsq,dbKup,dbKlo,...
dbrup,dbrlo,dbLlo,dbLup); %\t%.5f\t%.5f\t%.5f\t%.5f
%... outCmat(n,13),outCmat(n,14),outCmat(n,15),outCmat(n,16));
end
%*****DB analysis data end************************************************
%Add Intensities series to end of curve fit data
outIntens=[];
outIntens=zeros(384,dataLength);
intensBlob='';
tmBlob ='';
for j=1:dataLength %size(RawIntens,2) %size(outTseries,1)
if Ag(n)==0,Ag(n)=scan(s).Awindow;end
outIntens(n,j)= RawIntens(n,j)/Ag(n);
if isequal(opt,'Res')||isequal(opt,'Both')
fprintf(fid, '\t%.5f', outIntens(n,j)); % Results print Intens
end
if isequal(opt,'DB')||isequal(opt,'Both')
if j<dataLength
intensBlob= strcat(intensBlob,num2str(outIntens(n,j)),';');
else
intensBlob= strcat(intensBlob,num2str(outIntens(n,j)));
end
if outTseries(j)<.0001,outTseries(j)=0;end
if j<dataLength
tmBlob= strcat(tmBlob,num2str(outTseries(j)),';');
else
tmBlob= strcat(tmBlob,num2str(outTseries(j)));
end
end %if DB
end %j
%***************************
% Results fprint***********
if isequal(opt,'Res')||isequal(opt,'Both')
for nn=1:numBlkCol %extend to col beyond longest rawDataSet
fprintf(fid, '\t');
end
%-----------------------------------------------
% UPDATE 14_0626 to writein ' ' if personnel fail to in their
% Masterplate sheet
if ~isnan(orfRep)
fprintf(fid, '\t%s', orfRep); %print OrfRep
else
fprintf(fid, '\t%s', ' ');
end
if ~isnan(specifics)
fprintf(fid, '\t%s', specifics);
else
fprintf(fid, '\t%s', ' ');
end
if ~isnan(strain)
fprintf(fid, '\t%s', strain);
else
fprintf(fid, '\t%s', ' ');
end
%-----------------------------------------------
%****************************
fprintf(fid, '\n');
ln=ln+1;
fprintf(fid,'%d\t',ln);
end
%****************************
%DB Raw Intensities and Timepoints
if isequal(opt,'DB')||isequal(opt,'Both')
fprintf(fid2, '\t%s\t%s',intensBlob,tmBlob );
%-------------------------------
% UPDATE 14_0626 to writein ' ' if personnel fail to in their
% Masterplate sheet
if ~isnan(orfRep)
fprintf(fid2, '\t%s',orfRep );
else
fprintf(fid2, '\t%s', ' ');
end
if ~isnan(specifics)
fprintf(fid2, '\t%s',specifics );
else
fprintf(fid2, '\t%s', ' ');
end
if ~isnan(strain)
fprintf(fid2, '\t%s',strain );
else
fprintf(fid2, '\t%s', ' ');
end
%---------------------------------
fprintf(fid2, '\n');
end %DB print
end %if ~isempty(outCmat)
end %c
end %r
end %p
end %s
if isequal(opt,'Res')||isequal(opt,'Both')
fclose(fid);
end
if isequal(opt,'DB')||isequal(opt,'Both')
fclose(fid2);
try
copyfile(DBfilename,DBupload)
catch ME
rep = getReport(ME, 'basic');
rep=strcat('Failed copyfile to ',DBupload,' -', rep);
errordlg(rep)
end
end %if DB
ln;
catch
errorNstdResults='Catch at line720 for printing ResultsStd'
end %try scan(1).plate(1).CFoutStd(1,1) to test for 2018 r_refined version
cd(w)
scriptComplete= "line724 "
msgbox(['Printing Script complete. Check !!Results sheets in ../PrintResults folder.'])

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workflow/templates/easy/EASYconsole.fig Executable file
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workflow/templates/easy/EASYconsole.m Executable file
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% Launch the MATLAB EASY console
% From EstartConsole.m
clear;
clc;
global openExpfile
global openExppath
global newExpfile
global newExppath
global SWnewExp
global ExpOutmat
global ExpPath
global matDir
global resDir
global wCodeDir
global fhconsole
global ImParMat
global scan
% Set working dir as the pwd
wCodeDir=pwd
% Try to enter WCodeDir
function returnHome
global wCodeDir
try
cd(wCodeDir)
catch
msgbox('Failed to enter selected default directory so starting search at root.');
if ispc
cd(fullfile('C:\'));
elseif (isunix | ismac)
cd(fullfile('/mnt/data'));
else
msgbox('Unknown platform')
end
end
% Init
function varargout = EASYconsole(varargin)
% initialize global variables for function EASYconsole
global ExpOutmat
global ExpPath
global fhconsole
global resDir
global wCodeDir
global ImParMat
% changing directory to wCodeDir
returnHome
%% GUI INTERFACE DESIGN %%
% beginning of GUI formation & design, see help GUI or help GUIDE in
% command window for more information
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @EASYconsole_OpeningFcn, ...
'gui_OutputFcn', @EASYconsole_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% GUI
% Easyconcole_OpeningFcn executes just before the EASYconsole GUI is made visible.
% This function has no output args, see OutputFcn.
% hObject--handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles--structure with handles and user data (see GUIDATA)
% varargin--input arguments to EASYconsole (see VARARGIN)
function EASYconsole_OpeningFcn(hObject, ~, handles, varargin)
global ExpOutmat
global ExpPath
global fhconsole
global resDir
global wCodeDir
global ImParMat
% Choose default command line output for EASYconsole
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
%Figure header, Toolbar, etc. Setup
fhconsole=gcf;
set(fhconsole,'Toolbar','none');
fhconsole=gcf;
if exist('resDir','var')&&~isempty(resDir)
set(fhconsole,'Name',strcat('EASYconsole- ',char(resDir)));
else
set(fhconsole,'Name','EASYconsole -Exp. Analysis NOT selected.')
end
% Output
% Outputs from this function are returned to the command line.
% varargout--cell array for returning output args (see VARARGOUT);
% hObject--handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles--structure with handles and user data (see GUIDATA)
function varargout = EASYconsole_OutputFcn(~, ~, handles)
% Get default command line output from handles structure
varargout{1} = handles.output;
%% CONSOLE BUTTON INTERFACES %%
% File Button Interface
function FileMenu_Callback(~, ~, ~)
returnHome
% Load Experiment Button Interface
function LoadExp_Callback(~, ~, ~)
returnHome
% New Experiment Button Interface
function NewExpDat_Callback(~, ~, ~)
global newExpfile
global newExppath
global SWnewExp
global ExpOutmat
global ExpPath
global matDir
global resDir
global wCodeDir
global fhconsole
global scan
% CREATE NEW EXPERIMENT %
try
questdlg('\fontsize{20} NAME the file and NAVIGATE to the directory with the image folders.','File Creation','OK', struct('Default','OK','Interpreter','tex'));
[newExpfile,newExppath] = uiputfile(' .mat');
SWnewExp=1;
returnHome
newExpfilePref= strrep(newExpfile,'.mat','');
resDirName=strcat('Results',datestr(now,29),newExpfilePref);
% creation of the Results file
if ~exist(fullfile(newExppath,resDirName,'matResults'))
mkdir (fullfile(newExppath,resDirName,'matResults'));
end
% assigning paths to global variables
resDir= fullfile(newExppath,resDirName);
matDir= fullfile(newExppath,resDirName,'matResults');
ExpOutmat=fullfile(matDir,strcat(datestr(now,29),newExpfile));
ExpPath= fullfile(newExppath);
% Added for 'parfor global' to preallocate 'scan' structure 20-0123
nlist=dir(fullfile(ExpPath,'*'));
nnn=0;
for n=1:size(nlist,1)
if (~isempty(str2num(nlist(n).name)))
nnn=nnn+1;
PnumLst(nnn)= (str2num(nlist(n).name));
sl(nnn,1)={(nlist(n).name)};
end
end
scanSize= size(sl,1);
scanMax= max(str2double(sl));
clear scan;
scan(scanMax)= struct(); %changed for parfor global 20_0118
save(ExpOutmat,'scan')
% create 'PrintResults' file
if ~exist(fullfile(ExpPath,resDirName,'PrintResults'))
mkdir(fullfile(ExpPath,resDirName,'PrintResults'));
end
% copy 'figs' file and place it in ExpPath Directory
if ~exist(fullfile(ExpPath,resDirName,'figs'))
copyfile((fullfile(wCodeDir,'figs')), (fullfile(ExpPath,resDirName,'figs')))
end
% create 'CFfigs' file
if ~exist(fullfile(ExpPath,resDirName,'CFfigs'))
mkdir(fullfile(ExpPath,resDirName,'CFfigs'));
end
% copy 'PTmats' file and place it in ExpPath Directory
if ~exist(fullfile(ExpPath,resDirName,'PTmats'))
copyfile((fullfile(wCodeDir,'PTmats')), (fullfile(ExpPath,resDirName,'PTmats')))
end
% create 'Fotos' file
if ~exist(fullfile(ExpPath,resDirName,'Fotos'))
mkdir(fullfile(ExpPath,resDirName,'Fotos'));
clear sbdg % reduce possible retention of a previous job sdbg
sbdg= cell(1,scanMax);
save((fullfile(resDir,'Fotos','Nbdg')),'sbdg');
end
% create backup 'Fotos' file
if ~exist(fullfile(ExpPath,resDirName,'Fotos','BkUp'))
mkdir(fullfile(ExpPath,resDirName,'Fotos','BkUp'));
end
catch ME
returnHome
disp('Error Creating a New Experiment. Loc: EASYconsole.m Lines 106-197')
end
% set the title for fhconsole depending on existence
if exist('resDir','var')&&~isempty(resDir)
set(fhconsole,'Name',strcat('EASYconsole- ',char(resDir)))
else
set(fhconsole,'Name','EASYconsole -Exp. Analysis NOT selected.')
end
% Load a previous experiment
% Load Experiment Analysis directory/file structure
function LoadDatFile_Callback(~, ~, ~)
global openExpfile
global openExppath
global SWnewExp
global ExpOutmat
global ExpPath
global matDir
global resDir
global wCodeDir
global fhconsole
global ImParMat
returnHome
questdlg('\fontsize{20} Load file from ExpJobs/YourJob/YourResults/matResults','File Creation','OK', struct('Default','OK','Interpreter','tex'));
[openExpfile,openExppath] = uigetfile('.mat','Open Experiment folder and data storage .mat file name','MultiSelect','off');
SWnewExp=0;
ExpOutmat= fullfile(openExppath,openExpfile);
load(ExpOutmat);
cd(openExppath)
cd ..;
resDir=pwd;
cd ..;
ExpPath=pwd;
cd (wCodeDir)
ExpPath= fullfile(ExpPath);
if isfolder(fullfile(openExppath, '..','..','1')) %If Inovation Vrobot Then
if exist(fullfile(resDir,'PTmats','NImParameters.mat'))
load(fullfile(resDir,'PTmats','NImParameters.mat'));
else
curDir=pwd;
returnHome
load NImParameters.mat
cd(curDir)
end
else %If Epson 10Plate Scans Then>
if exist(fullfile(resDir,'PTmats','ImParameters.mat'))
load(fullfile(resDir,'PTmats','ImParameters.mat'));
else
curDir=pwd;
returnHome
load ImParameters.mat
cd(curDir)
end
end
matDir= fullfile(openExppath,'\');
mkdir(fullfile(matDir,'BkUp'));
% create supporting files
if ~exist(fullfile(resDir,'PrintResults'))
mkdir(fullfile(resDir,'PrintResults'));
end
if ~exist(fullfile(resDir,'figs'))
mkdir(fullfile(resDir,'figs'));
end
if ~exist(fullfile(resDir,'CFfigs'))
mkdir(fullfile(resDir,'CFfigs'));
end
if ~exist(fullfile(resDir,'PTmats'))
mkdir(fullfile(resDir,'PTmats'));
end
if ~exist(fullfile(resDir,'Fotos'))
mkdir(fullfile(resDir,'Fotos'));
end
catch
returnHome
end
clear scan
if exist('resDir','var')&&~isempty(resDir)
fhconsole= gcf;
set(fhconsole,'Name',strcat('EASYconsole- ',char(resDir)))
else
set(fhconsole,'Name','EASYconsole -Exp. Analysis NOT selected.')
end
%% CALLBACKS %%
% callback for the 'Run' in the dropdown menu
function run_Callback(~, ~, ~)
returnHome
function runPlateMapPintool_Callback(~, ~, ~)
returnHome
try
NImapPT
catch ME
returnHome
EASYconsole
end
function NImCFcombo_Callback(~, ~, ~)
returnHome
try
par4Gbl_Main8c
catch
returnHome
EASYconsole
end
function runPlateImAnal_Callback(~, ~, ~)
returnHome
try
NImStartupOnly
catch ME
returnHome
EASYconsole
end
function PlateCFit_Callback(~, ~, ~)
returnHome
try
NCstart
catch ME
returnHome
end
function GenPrintouts_Callback(~, ~, ~)
function uploadExcelMP2DB_Callback(~, ~, ~)
function runDMPexcel_Callback(~, ~, ~)
try
DMPexcel2mat
catch ME
returnHome
EASYconsole
end
function runResults_DBcombo_Callback(~, ~, ~)
try
DgenResults %similar but semicolons removed to restore so cmdLine display info.
%DgenResults %par4global -convert 1x1cell of 384cells to be like previous 1x384 cells CFparameter
catch ME
disp('Error in DgenResults')
returnHome
EASYconsole
end
function Tools_Callback(~, ~, ~)
function runOverlayPlots_Callback(~, ~, ~)
returnHome
try
DoverlayPlots2
returnHome
EASYconsole
catch ME
returnHome
EASYconsole
end
function runFotoStrip_Callback(~, ~, ~)
returnHome
try
F_NImStartup_CentCir
returnHome
EASYconsole
catch ME
returnHome
EASYconsole
end
function runDisplayFig_Callback(~, ~, ~)
returnHome
try
UfigDisplay
catch ME
returnHome
EASYconsole
end
function runViewParameters_Callback(~, ~, ~)
returnHome
try
% This was blank in original
catch ME
returnHome
EASYconsole
end
function QkviewN_Callback(~, ~, ~)
global ExpPath
returnHome
try
try
cd fullfile(ExpPath)
catch
if ispc cd c:\
else
cd (fullfile('~'));
end
end
QkviewImages
catch ME
returnHome
EASYconsole
end
function CFdisplay_Callback(~, ~, ~)
returnHome
try
NCsingleDisplay
returnHome
EASYconsole
catch ME
returnHome
EASYconsole
end

497
workflow/templates/easy/NCdisplayGui.m Executable file
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%% CALLED WHEN ACCESSING 'CurveFit Display' %%
function [scLst, row, col] = NCdisplayGui(eDir) %(ExpPath)
%global ExpPath
%global expDir
xPos=0.05;
btnWid=0.10;
btnHt=0.05;
spacing=0.02;% Spacing between the button and the next command's label
%hSpot= figure;
%figure
%====================================
% The ADD Groups button
btnNumber=1;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
%
row=1;
hedit = uicontrol(...
'Style', 'edit',...
'String',row,...
'Units','normalized',...
'Position', btnPos,... % [.002 .70 .08 .10],...
'callback',{@editRowNum}); % 'Position', [5 100 60 20])
function editRowNum(source,~)
user_entry = str2double(get(source,'string'));
if (isnan(user_entry)||(user_entry<0)||(user_entry>17) )
errordlg('Enter a Row between 1 and 16','Bad Input','modal')
return
end
row= user_entry;
end
%-------------------222222-----------
%
btnNumber=2;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
col= 1;
hedit = uicontrol(...
'Style', 'edit',...
'String',col,...
'Units','normalized',...
'Position', btnPos,... % [.002 .70 .08 .10],...
'callback',{@entryColNum}); % 'Position', [5 100 60 20])
function entryColNum(source,~)
user_entry = str2double(get(source,'string'));
if (isnan(user_entry)||(user_entry<0)||(user_entry>25))
errordlg('Enter a Column between 1 and 24','Bad Input','modal')
return
end
col= user_entry;
end
%}
%*************************************************************
%Ncode 12_0120 for reading in numeric folder names
nlist=dir(fullfile(eDir,'*')); %(ExpPath,'*'));
nnn=0;
for n=1:size(nlist,1)
if (~isempty(str2num(nlist(n).name)))
nnn=nnn+1;
PnumLst(nnn)= (str2num(nlist(n).name));
slst(nnn,1)={(nlist(n).name)};
end
end
hListbox = uicontrol(...
'Style', 'listbox',...
'String',sort(slst),...
'value',[],...
'max',1000,...
'min',1,...
'Units','normalized',...
'Position', [.40 .40 .10 .60],...
'callback',{@load_listbox}); %'uiresume(gcbf)'); 'Position', [5 100 60 20])
function load_listbox(source,~)
userIndx = (get(source,'value'));
userStr = (get(source,'string'));
%scLstIndx= str2num(char(strrep(userStr(userIndx), 'Scan', '')))
user_entry=userStr(userIndx);
scLst= user_entry;
end
%*****************************************************************
%-------------------10 10 10 10-----------
btnNumber=10;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
hedit8 = uicontrol(...
'Style', 'pushbutton',...
'String',{'Continue'},...
'Units','normalized',...
'Position', btnPos,...
'callback','uiresume(gcbf)');
%------------------------------
%***************************************************************
% {
%********LABELS******************************
% The Labels
xLPos=0.175;
yPos=0;
btnWid=0.20;
% Removed Not needed for Ncode ImRobot
lblNumber=1;
yPos=0.85-(lblNumber-1)*(btnHt+spacing);
btnPos=[xLPos yPos-spacing btnWid btnHt];
htxt = uicontrol(...
'Style', 'text',...
'String','Row',...
'Units','normalized',...
'Position', btnPos);
%-------------------222222-----------
lblNumber=2;
yPos=0.85-(lblNumber-1)*(btnHt+spacing);
btnPos=[xLPos yPos-spacing btnWid btnHt];
htxt = uicontrol(...
'Style', 'text',...
'String','Column',...
'Units','normalized',...
'Position', btnPos);
% Not needed for Ncode ImRobot
uiwait(gcf);
end %function end $$$$$
%}
%{
%-------------------333333-----------
lblNumber=3;
yPos=0.85-(lblNumber-1)*(btnHt+spacing);
btnPos=[xLPos yPos-spacing btnWid btnHt];
htxt = uicontrol(...
'Style', 'text',...
'String','BG Threshold (%above) Detection',...
'Units','normalized',...
'Position', btnPos);
%-------------------4-----------
lblNumber=4;
yPos=0.85-(lblNumber-1)*(btnHt+spacing);
btnPos=[xLPos yPos-spacing btnWid btnHt];
htxt = uicontrol(...
'Style', 'text',...
'String','SpotDetThres(1-60%)',...
'Units','normalized',...
'Position', btnPos);
%-------------------55555-----------
lblNumber=5;
yPos=0.85-(lblNumber-1)*(btnHt+spacing);
btnPos=[xLPos yPos-spacing btnWid btnHt];
htxt = uicontrol(...
'Style', 'text',...
'String','Radius',... %'String','Width',...
'Units','normalized',...
'Position', btnPos);
%-------------------66666-----------
lblNumber=6;
yPos=0.85-(lblNumber-1)*(btnHt+spacing);
btnPos=[xLPos yPos-spacing btnWid btnHt];
htxt = uicontrol(...
'Style', 'text',...
'String','Dither',...
'Units','normalized',...
'Position', btnPos);
%-------------------77777-----------
lblNumber=7;
yPos=0.85-(lblNumber-1)*(btnHt+spacing);
btnPos=[xLPos yPos-spacing btnWid btnHt];
htxt = uicontrol(...
'Style', 'text',...
'String','SearchRange',...
'Units','normalized',...
'Position', btnPos);
%-------------------88888-----------
%{
lblNumber=8;
yPos=0.85-(lblNumber-1)*(btnHt+spacing);
btnPos=[xLPos yPos-spacing btnWid btnHt];
htxt = uicontrol(...
'Style', 'text',...
'String','Blank2',...
'Units','normalized',...
'Position', btnPos);
%----------------------------------------
%}
%}
%{
%-------------------66666-----------
btnNumber=6;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
srcExtendFactor=ImParMat(7);
hedit = uicontrol(...
'Style', 'edit',...
'String',srcLoIntensThres,...
'Units','normalized',...
'Position', btnPos,...
'callback',{@entryExtendFactor});
function entryExtendFactor(source,eventdata)
user_entry = str2double(get(source,'string'));
if (isnan(user_entry)||(user_entry<1.8)||(user_entry>4.0))
errordlg('You must enter a numeric value between 1.8 and 2.1','Bad Input','modal')
return
end
ExtendFactor=user_entry
ImParMat(7)= ExtendFactor
ExtendFactor
end
%}
%{
%-------------------333333-----------
btnNumber=3;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
srcBGthreshold=ImParMat(3);
hedit = uicontrol(...
'Style', 'edit',...
'String',srcBGthreshold,...
'Units','normalized',...
'Position', btnPos,... % [.002 .70 .08 .10],...
'callback',{@entryBGthreshold}); % 'Position', [5 100 60 20])
function entryBGthreshold(source,eventdata)
user_entry = str2double(get(source,'string'));
if (isnan(user_entry)||(user_entry<1)||(user_entry>100))
errordlg('Enter a numeric value between 1 and 100 percent to produce a Background Threshold value as a percent above the time series average background for each spot.','Bad Input','modal')
return
end
BGthresInput=user_entry
ImParMat(3)= BGthresInput
BGthresInput
end
%-------------------444444-----------
btnNumber=4; %Enter spot detection threshold (lock-in Image frame)
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
srcSpotThres=ImParMat(4);
hedit = uicontrol(...
'Style', 'edit',...
'String',srcSpotThres,...
'Units','normalized',...
'Position', btnPos,...
'callback',{@entrySpotThres});
function entrySpotThres(source,eventdata)
user_entry = str2double(get(source,'string'));
if (isnan(user_entry)||(user_entry<1)||(user_entry>60))
errordlg('You must enter a numeric value between 1 and 60','Bad Input','modal')
return
end
spotThres=user_entry
ImParMat(4)= spotThres
spotThres
end
%
%---------555555 Radius Entry After Sept.2014---------------------------------**
btnNumber=5;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
srcRadius=ImParMat(10);
hedit = uicontrol(...
'Style', 'edit',...
'String',srcRadius,...
'Units','normalized',...
'Position', btnPos,... % [.002 .70 .08 .10],...
'callback',{@entryRadius}); % 'Position', [5 100 60 20])
function entryRadius(source,eventdata)
user_entry = str2double(get(source,'string'));
if (isnan(user_entry)||(user_entry<12)||(user_entry>17))
errordlg('You must enter a numeric value between 12 and 17','Bad Input','modal')
return
end
Radius=user_entry
ImParMat(10)= Radius
Radius
end
%---------555555 Width Entry prior the Sept.2014---------------------------------**
%{
btnNumber=5;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
srcWidth=ImParMat(5);
hedit = uicontrol(...
'Style', 'edit',...
'String',srcWidth,...
'Units','normalized',...
'Position', btnPos,... % [.002 .70 .08 .10],...
'callback',{@entryWidth}); % 'Position', [5 100 60 20])
function entryWidth(source,eventdata)
user_entry = str2double(get(source,'string'));
if (isnan(user_entry)||(user_entry<5)||(user_entry>41))
errordlg('You must enter a numeric value between 5 and 40','Bad Input','modal')
return
end
Width=user_entry
ImParMat(5)= Width
Width
end
%}
%-------------------66666 Dither unnecessary after Sept.2014-----------
btnNumber=6;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
srcDither= ImParMat(6);
hedit = uicontrol(...
'Style', 'edit',...
'String',srcDither,...
'Units','normalized',...
'Position', btnPos,...
'callback',{@entryDither});
function entryDither(source,eventdata)
user_entry = str2double(get(source,'string'));
if (isnan(user_entry)||(user_entry<0)||(user_entry>5))
errordlg('You must enter a numeric value between 1 and 4','Bad Input','modal')
return
end
Dither=user_entry
ImParMat(6)= Dither
Dither
end
%-------------------77777----------- Added July 7,2015 to allow Search Range constraint
btnNumber=7;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
try
CSrchRange=ImParMat(12);
CSrchRng=ImParMat(12)
catch %Legacy default value was 18 before being made a user input variable (ImParMat(12)). A preferable value now might be 12 or 14.
CSrchRange=18;
ImParMat(12)=18
CSrchRng=ImParMat(12)
end
%{
if size(scLst)>1
CSrchRange=ImParMat(12);
else
try
CSrchRange=CSearchRange(str2double(scLst))
catch
CSrchRange=ImParMat(12);
end
end
%}
hSearchRange = uicontrol(...
'Style', 'edit',...
'String',CSrchRange,...
'Units','normalized',...
'Position', btnPos,...
'callback',{@CsearchRange});
function CsearchRange(source,eventdata)
user_entry = str2double(get(source,'string'));
if (isnan(user_entry)||(user_entry<1)||(user_entry>50)) %originally 18; 19_0729 increased
errordlg('You must enter a numeric value between 1 and 18 12->18 recommended. (ImParMat(12)))','Bad Input','modal')
return
end
CSrchRng=user_entry
end
%-------------------77777-----------
%{
btnNumber=7;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
srcExtend=ImParMat(7);
hedit = uicontrol(...
'Style', 'edit',...
'String',srcExtend,...
'Units','normalized',...
'Position', btnPos,...
'callback',{@entryExtend});
function entryExtend(source,eventdata)
user_entry = str2double(get(source,'string'));
if (isnan(user_entry)||(user_entry<-0.10)||(user_entry>0.4))
errordlg('You must enter a numeric value between 0 and 0.4. 0.10 recommended','Bad Input','modal')
return
end
extend=user_entry
ImParMat(7)= extend
extend
end
%-------------------888888-----------
btnNumber=8;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
%ImParMat(8)=1;
srcpointExtend=ImParMat(8);
hedit = uicontrol(...
'Style', 'edit',...
'String',srcpointExtend,...
'Units','normalized',...
'Position', btnPos,...
'callback',{@entrypointExtend});
function entrypointExtend(source,eventdata)
user_entry = str2double(get(source,'string'));
user_entry= floor(user_entry);
if (isnan(user_entry)||(user_entry<-3)||(user_entry>5))
errordlg('You must enter an integer value between 0 and 5. 1 recommended','Bad Input','modal')
return
end
pointExtend=user_entry
ImParMat(8)= pointExtend
pointExtend
end
%}
%-------------------999999-----------
btnNumber=9;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
hedit = uicontrol(...
'Style', 'popupmenu',...
'String',{'GrowthArea','FixedArea'},...
'Units','normalized',...
'Position', btnPos,...
'callback',{@grwArea});
function grwArea(source,eventdata)
str = get(source, 'String');
val = get(source,'Value');
% Set current data to the selected data set.
switch str{val};
case 'GrowthArea' ;% User selects Peaks.
SWgrowthArea = 1
case 'FixedArea' % User selects Membrane.
SWgrowthArea = 0
end
end
%}
%global SWsingleSc
%global SWgrowthArea
%global selScan
%global scan
%global scLst
%global ImParMat
%global CSearchRange
%global CSrchRng
%global defImParMat
%global fhImRun
%global fhconsole
%global resDir
%global ExpOutmat
%global numRows;
%global numCols;

275
workflow/templates/easy/NCfitImCFparforFailGbl2.m Executable file
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%% CALLED BY par4GblFnc8c.m %%
function [par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanIntensELr,par4scanCFparameters,par4scanCFdate,outC,outCstd]= ...
NCfitImCFparforFailGbl2(parMat,times, values, timeOffsets, fileSuffix, AUCfinalTime, ~, spotAreas, outputDirectory, ~,~, sols, ~) %,scan)
%Preallocation for parfor loop**********************************
st(1,1:size(times,2))= 1111;
resMat(1,1:27)= 0;
resMatStd= resMat;
outC= zeros(384,27);
outCstd= zeros(384,27);
for m=1:384
pa{m}= st;
par4scanCFparameters{m}= parMat;
par4scanCFdate{m}= datestr((now),31);
end
par4scanselTimesStd= pa;
par4scanselIntensStd= pa;
par4scanTimesELr= pa;
par4scanIntensELr= pa;
par4resMat= zeros(384,27);
par4resMatStd= zeros(384,27);
%****************************************************************
%*****************Begin the Spot(cultures) loop****************************
for ii= 1:384 %startSpot:numCultures
%parfor ii= 1:384 %startSpot:numCultures
ii; %%%db print out the culture number
timepts= [];
currValues=[];
currSpotAreas=[];
currSpotArea=[];
dataMatrix=[];
selTimesStd=[]; %191024 parfor
selIntensStd=[]; %191024 parfor
FiltTimesELr=[]; %191024 parfor
NormIntensELr=[]; %191024 parfor
% add offset...1 offset PER PLATE
timepts = times + timeOffsets; %(floor((ii-1)/arrayFormat) + 1);
currValues = values(ii,:); %change values(spotNum,:);
% get spot areas for this culture
currSpotArea = spotAreas(:,ii);
% just use the area at the last time point
%currSpotArea = currSpotAreas(1);
%--------------------------------------------------------------
%Preallocate to accomodate parfor loop **************************
resMatStd= zeros(1,27);
resMat= zeros(1,27);
currNormIntens = currValues/currSpotArea;
tmpx=find(currNormIntens>5); %15jh % 2.3);
validSpot=true;
if(isempty(tmpx) || (length(tmpx)<3))
validSpot= false;
normIntens= currNormIntens;
filterTimes= timepts; %filterTimes; %currTimes;
selTimesStd= timepts;
selIntensStd= currNormIntens;
FiltTimesELr= timepts;
NormIntensELr= currNormIntens;
else
%*******************************************************
%NCfilImCF
%NCfilImCF.m called from NCfitImCF.m line 119*******************
%Preallocate incase something bails in NCscurImCFparfor
resMatStd= zeros(1,27);
resMat= zeros(1,27);
hold off %09_0704
dataMatrix=[];
K=0;r=0;l=0;Klow=0;Kup=0;rlow=0;rup=0;llow=0;lup=0;AUC=0;MSR=0; rsquare=0;
bl=0;
Tpt1=0; numFitTpts =0;thresGT2=0;minTime=0;fitbl=0; %diagnostic outputs only
timepts= timepts; %timepts= currTimes; parfor
normIntens= currNormIntens;
dataMatrix= []; %parfor move clear from NCfitImCF...m
loIntensThres=parMat(4);
stdLoIntLim=parMat(5);
%******Begin basic filter**********
%[loInten Thres,stdbased Trim before Scurve start, and dropout detection]
if(max(normIntens) > 2.29)
threshold = loIntensThres; %1.9; %Increase this value to reduce low data point (flag=2)
else
threshold = 0;
end
dropThreshold= -0.0001* max(normIntens);
%Initialize dataMatrix**********************************
dataMatrix(1,:)=timepts;
dataMatrix(2,:)=normIntens;
dataMatrix(3,:)= ones;
dataMatrix(4,:)=normIntens;
%Determine a mean Intensity Index point and assoc'd TimePt
a= min(normIntens(normIntens>=0)); %(find(normIntens>=0)));
b= max(normIntens(normIntens>=0)); %(find(normIntens>=0)));
c= 0.5*(b-a);
d= b-c;
meanIntIndPt= find(normIntens>d,1);
meanInt= normIntens(meanIntIndPt);
meanTime= times(meanIntIndPt);
%**********************************************************
%**************************************************************************
% NCLoIntstdTrim
%NCLoSstdTrim.m called by NCfilImCF and NCfil.m
flg1=0;
loScurvLim=stdLoIntLim; %
loStimeN=1;
last2n=1;
stdDev= [];
nrmIntens0= normIntens;
for n=1:meanIntIndPt
if nrmIntens0(n)<=0
nrmIntens0(n)=0;
end
if(nrmIntens0(n)<threshold)
if (loStimeN-2)>0,dataMatrix(3,1:(n-2))= 2; %add to lowIntensity cull flags, the pre S cull data
else dataMatrix(3,1:n)= 2;end
dataMatrix(3,1:(n-2))= 2;
last2n=n;
end
if n<(length(nrmIntens0)-3)
x=nrmIntens0(n:(n+3));
stdDev(n)=std(x);
if (stdDev(n)<loScurvLim && flg1~=1)
loStime=timepts(n);
loStimeN=n;
end
if stdDev(n)>6 ,flg1=1;end %detect S curve rise->stop stdLoInt detection
end
end %end for
if (loStimeN-2)>0,dataMatrix(3,1:(loStimeN-2))= 2; %add to lowIntensity cull flags, the pre S cull data
else dataMatrix(3,1:(loStimeN-2))= 2;end
qcutoff=2;
qind=find(normIntens>2); %,:,'first');
if ~isempty(qind(3)), qcutoff=qind(3);end
[minInt,I]= min(normIntens(2:qcutoff));
bl=minInt;
minTime=dataMatrix(1,I); %diagnostic output only
if (length(qind)>5)&&I>1,dataMatrix(3,1:(I-1))=5; end
tGT2Flg=0;
for n=1:length(normIntens)
dataMatrix(4,n)=normIntens(n)-bl;
if n>I && dataMatrix(4,n)>=2 && tGT2Flg==0
thresGT2=n;thresGT2Tm=dataMatrix(1,n);tGT2Flg=1;
end %diagnostic output only
end
resMat(18)= bl;
resMatStd(18)= bl;
resMatStd(20)= minTime;
resMat(20)= minTime;
%&&&&&&&&&&&&&&&&&&&&&&& &&&&&&&&&&&&&&&&&&&&&&&&
%*********************************************************
%DropOut cull section(single drop points)*******************
DropOutStartPt=length(normIntens);
for n=1:length(normIntens)
if(n>1)
if(((normIntens(n)- normIntens(n-1))< dropThreshold))&& ...
(n > max(meanIntIndPt,thresGT2) )
dataMatrix(3,n)= 6;
end
end
end
%??????should/could this be removed as recreated in%NCscurImCF_3parfor.m????????????????????
%Post Stdtest cull for low intensities inclusion of additional low value points
%selTimes= [--,--] %don't know size before as it is a filtered output
tmpIndx= 0;
for n=1:length(normIntens)
if (dataMatrix(3,n)==1)
tmpIndx= tmpIndx+1;
selTimes(tmpIndx)= dataMatrix(1,n); %selTimes(nn)= dataMatrix(1,n);
selIntens(tmpIndx)= dataMatrix(4,n); %selIntens(nn)= dataMatrix(4,n);
end
end
selTimes=selTimes';
selIntens=selIntens';
%???????????????????????????????????????????????????
%**********End Basic filter******************
%******************************************************
filtNormIntens=normIntens;
dataMatrix0= dataMatrix;
filterTimes= timepts; %parfor
%_____________________________________________________________
%*******************************************
%NCscurImCF
%NCscurImCF_1
%NCscurImCF_2
%NCscurImCF_3
%NCscurImCF_3parfor
%NCscurImCF_3parfor(dataMatrix, AUCfinalTime)
%dataMatrix %debugging parfor gbl ok 85.7145; 126.4579,6, 124.5264 37tPt
%adsfj %debugging parfor gbl
[resMatStd, resMat, selTimesStd, selIntensStd, FiltTimesELr, NormIntensELr] =...
NCscurImCF_3parfor(dataMatrix0, AUCfinalTime, currSpotArea, sols, bl, minTime);
end % end JUMP OVER associated with if(find(intensities>1000)<5)
%resMatStd
%asdf
%To accommodate parfor can't use global 'scan' variable 191002================
% {
par4scanselTimesStd{ii}= selTimesStd; %timepts'; %filterTimes';
par4scanselIntensStd{ii}= selIntensStd; %normIntens';
par4scanTimesELr{ii}= FiltTimesELr; %19_1021 preserve for CurveDisplay and EZview
par4scanIntensELr{ii}= NormIntensELr; %19_1021 preserve for CurveDisplay and EZview
%}
%$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
%************* striped down OutCell code was put back into NCfitImCF
outC(ii,:)= resMat; %{ii, par4resMat};
outCstd(ii,:)= resMatStd; %{ii, par4resMatStd};
end %Multispot parfor ii loop end PARFOR LOOP END##############################################################################
%###############################################################################################################################
%###############################################################################################################################
%outC
%*********************************19_1001***********************************
%To accomodate parfor copy par4scan thru global p4 functions inside of
%parfor loop --then outside to par4Gbl_Main8b.m
%**************************************************************************
fileExt = '.txt';
filePrefix = 'FitResultsComplete_';
fileNamePlate = [filePrefix fileSuffix fileExt];
fileName= fullfile(outputDirectory, fileNamePlate); %[outputDirectory fileNamePlate];
fid = fopen(fileName,'w');
fprintf(fid, 'Fit Results Complete\n');
%fprintf(fid, 'Num.\tAUC\tMSR\tK\tr\tl\tR-squared\tK-lower\tK-upper\tr-lower\tr-upper\tl-upper\tl-lower\tArea\tLastInten\tSpineMaxRateTimePt\tLastFitTimePt\n');
fclose(fid);
end %function end
%&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&
%##########################################################################

437
workflow/templates/easy/NCscurImCF_3parfor.m Executable file
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%% CALLED BY NCfitImCFparforFailGbl2.m %%
function [resMatStd, resMat, selTimesStd, selIntensStd, FiltTimesELr, NormIntensELr] =...
NCscurImCF_3parfor(dataMatrix, AUCfinalTime, currSpotArea, sols, bl, minTime)
%Major revision for Early-Late data cuts to improve accuracof 'r'. Removed legacy iterative method.
%Significant Modification for Parfor
%***************************************************************
%##########################################################################
%******************************************* New Stage 1***************************************************************
%Preallocate
resMatStd= zeros(1,27);
resMat= zeros(1,27);
%Set internal variables sent to matlab fit function
me=200;
meL=750;
mi=25; %50
miL=250;
%***********************************
rmsStg1=0;
rmsStg1I(1)= 0;
slps=1;
filterTimes=[];
normIntens=[];
nn=1;
numFitTpts=0;
%Build filterTimes and normIntens from spot dataMatrix selection codes produced in filter section
for n=1:size(dataMatrix,2)
if (((dataMatrix(3,n)==1))||(dataMatrix(3,n)==3)||(dataMatrix(3,n)==2)...
||(dataMatrix(3,n)==0))
filterTimes(nn)= dataMatrix(1,n);
normIntens(nn)=dataMatrix(4,n);
nn=nn+1;
end
end
%------------------------------------------------------------------
%++++++++++++++++++++++++++++++++++++++++
filterTimes=filterTimes';
selTimesStd=filterTimes;
normIntens=normIntens';
selIntensStd=normIntens;
%normIntens %debugging parfor gbl 200330 good values
%afgj
lastTptUsed= 1;
lastIntensUsed= 1;
thresGT2TmStd=0;
try
lastTptUsed=max(filterTimes);
lastIntensUsed=normIntens(length(normIntens));
lastIntensUsedStd= lastIntensUsed;
lastTptUsedStd= lastTptUsed;
Tpt1Std= filterTimes(1);
numFitTptsStd=nnz((normIntens(:)>=0)==1);
thresGT2 = find(((normIntens(:)>2)==1), 1);
if isempty(thresGT2)
thresGT2TmStd=0;
else
thresGT2TmStd = filterTimes(thresGT2);
end
numTptsGT2Std = nnz((normIntens(:)>=2)==1); %nnz(filterTimes(find(filterTimes>=thresGT2Tm)));
K_Guess = max(normIntens);
numTimePts = length(filterTimes);
opts = fitoptions('Method','Nonlinear','Robust','On',...
'DiffMinChange',1.0E-11,'DiffMaxChange',0.001,...
'MaxFunEvals',me, 'MaxIter', mi, 'TolFun', 1.0E-12, 'TolX', 1.0E-10, 'Lower', [K_Guess*0.5,0,0], 'StartPoint', [K_Guess,filterTimes(floor(numTimePts/2)),0.30], 'Upper', [K_Guess*2.0,max(filterTimes),1.0],'Display','off');
ftype = fittype('K / (1 + exp(-r* (t - l )))','independent','t','dependent',['K','r','l'],'options',opts);
% carry out the curve fitting process
[fitObject, errObj] = fit(filterTimes,normIntens,ftype);
coeffsArray = coeffvalues(fitObject);
rmsStg1=errObj.rsquare;
rmsStg1I(slps)= errObj.rsquare;
sDat(slps,1)=errObj.rsquare;
K = coeffsArray(1); sDat(slps,2)= coeffsArray(1); % Carrying Capacity
l = coeffsArray(2); sDat(slps,3)= coeffsArray(2); %lag time
r = coeffsArray(3); sDat(slps,4)= coeffsArray(3); % rateS
% integrate (from first to last time point)
numVals = size(filterTimes);
numVals = numVals(1);
t_begin = 0;
t_end = AUCfinalTime;
AUC = (K/r*log(1+exp(-r*(t_end-l)))-K/r*log(exp(-r*(t_end-l)))) - (K/r*log(1+exp(-r*(t_begin-l)))-K/r*log(exp(-r*(t_begin-l))));
MSR = r;
rsquare = errObj.rsquare;
confObj = confint(fitObject,0.9); % get the 90% confidence
NANcond=0; stdNANcond=0; %stdNANcond added to relay not to attempt ELr as there is no curve to find critical point
confObj_filtered=confObj;
Klow = confObj(1,1); sDat(slps,5)=confObj(1,1);
Kup = confObj(2,1); sDat(slps,6)=confObj(2,1);
llow = confObj(1,2); sDat(slps,7)=confObj(1,2);
lup = confObj(2,2); sDat(slps,8)=confObj(2,2);
rlow = confObj(1,3); sDat(slps,9)=confObj(1,3);
rup = confObj(2,3); sDat(slps,10)=confObj(2,3);
if(isnan(Klow)||isnan(Kup)||isnan(llow)||isnan(lup)||isnan(rlow)||isnan(rup))
NANcond=1; stdNANcond=1; %stdNANcond added to relay not to attempt ELr as there is no curve to find critical point
end
%rup %debugging parfor gbl 200330
%Klow
%asdfjj114
% {
catch %ME
% if no data is given, return zeros
AUC = 0;MSR = 0;K = 0;r = 0;l = 0;rsquare = 0;Klow = 0;Kup = 0;
rlow = 0;rup = 0;lup = 0;llow = 0;
NANcond=1; stdNANcond=1; %stdNANcond added to relay not to attempt ELr as there is no curve to find critical point
end %end Try
%}
if (exist('K','var')&& exist('r','var') && exist('l','var'))
t = (0:1:200);
Growth = K ./ (1 + exp(-r.* (t - l )));
fitblStd= min(Growth); %jh diag
end
cutTm(1:4)= 1000; %-1 means cuts not used or NA
%{
l %debugging parfor
K
r
Klow
k
%}
%***Preserve for ResultsStd+++++++++++++++++++++++++++++
resMatStd(1)= AUC;
resMatStd(2)= MSR;
resMatStd(3)= K;
resMatStd(4)= r;
resMatStd(5)= l;
resMatStd(6)= rsquare;
resMatStd(7)= Klow;
resMatStd(8)= Kup;
resMatStd(9)= rlow;
resMatStd(10)= rup;
resMatStd(11)= llow;
resMatStd(12)= lup;
resMatStd(13)= currSpotArea;
resMatStd(14)= lastIntensUsedStd; %filtNormIntens(length(filtNormIntens));
%spline fit unneccessary and removed;therefore No maxRateTime assoc'd w/spline fit
%try
%resMatStd(15)= maxRateTime;
%catch
maxRateTime= 0; %[]; %Std shows []; ELr shows 0; %parfor
resMatStd(15)= 0; %maxRateTimestdMeth;
%end
resMatStd(16)= lastTptUsedStd; %filterTimes(length(filterTimes));
if isempty(Tpt1Std)
Tpt1Std= 777; %0.000002; %
end
resMatStd(17)= Tpt1Std;
resMatStd(18)= bl; %perform in the filter section of NCfitImCFparfor
resMatStd(19)= fitblStd; %Taken from NCfil... and not affected by NCscur...changes
resMatStd(20)= minTime; %Not affected by changes made in NCscur...for refined 'r'
resMatStd(21)= thresGT2TmStd;
resMatStd(22)= numFitTptsStd;
resMatStd(23)= numTptsGT2Std;
resMatStd(24)= 999; %The Standard method has no cuts .:.no cutTm
resMatStd(25)= 999;
resMatStd(26)= 999;
resMatStd(27)= 999;
%if SwitchEvsEL==3 %Remove 'SwitchEvsEL==...' temporary SWITCH when Hartman decides what he wants
%*********************************************************************************
%ELr New Experimental data through L+deltaS Logistic fit for 'Improved r' Fitting
%*********************************************************************************
FiltTimesELr= []; %{ii}= filterTimes;
NormIntensELr= []; %{ii}= normIntens;
normIntens= selIntensStd;
filterTimes= selTimesStd;
stdIntens= selIntensStd;
tmpIntens= selIntensStd;
stdTimes= selTimesStd;
if stdNANcond==0
%Determine critical points and offsets for selecting Core Data based on
%Standard curve fit run. Put diff into NImStartupImCF02.m calling source
%to reduce repeated execution since it doesn't change.
%fd4=diff(sym('K / (1 + exp(-r* (t - l )))'),4);
%sols=solve(fd4);
tc1= eval(sols(2));
tc2= eval(sols(3));
LL= l; %eval(sols(1)); %exactly the same as 'l' from std. fit method-Save time
rsTmStd= LL-tc1; %%riseTime (first critical point to L)
deltS= rsTmStd/2;
tc1Early= tc1-deltS; %AKA- tc1AdjTm %2*tc1 -LL
L_Late= LL+deltS;
tc1EdatPt= find(filterTimes>(tc1Early),1,'first');
cutTm(1)= filterTimes(2);
cutDatNum(1)= 2;
cutTm(2)= tc1Early;
cutDatNum(2)= tc1EdatPt-1;
L_LDatPt= find(filterTimes< L_Late,1,'last');
tc2LdatPt= find(filterTimes< tc2+rsTmStd,1,'last');
cutTm(3)= L_Late;
cutDatNum(3)= L_LDatPt;
%Select Core Data Set (Remove Early data before critical point)
ints=[];
ints(1:L_LDatPt-tc1EdatPt+2)= (tmpIntens(L_LDatPt));
ints(2:end)= tmpIntens(tc1EdatPt:L_LDatPt);
ints(1)= tmpIntens(1);
tms=[];
tms(1:L_LDatPt-tc1EdatPt+2)= (stdTimes(L_LDatPt));
tms(2:end)= stdTimes(tc1EdatPt:L_LDatPt);
tms(1)= stdTimes(1);
%-----------------------------------------------
%Include/Keep late data that define K *********
if length(tmpIntens(tc2LdatPt:end))> 4
KlastInts= tmpIntens(tc2LdatPt:end);
KlastTms= stdTimes(tc2LdatPt:end);
lengthKlast= length(tmpIntens(tc2LdatPt:end));
ints(end:(end+ lengthKlast-1))= KlastInts;
tms(end:(end+ lengthKlast-1 ))= KlastTms;
cutTm(4)= tc2+rsTmStd;
cutDatNum(4)= tc2LdatPt-1;
else
lengthKlast= length(tmpIntens(tc2LdatPt-1:end));
if lengthKlast>1
KlastInts= tmpIntens(end-(lengthKlast-1):end);
KlastTms= stdTimes(end-(lengthKlast-1):end);
ints(end:(end+ lengthKlast-1 ))= KlastInts;
tms(end:(end+ lengthKlast-1 ))= KlastTms;
end
cutTm(4)= stdTimes(tc2LdatPt-1);
cutDatNum(4)= tc2LdatPt-2; %length(stdTimes(end-(lengthKlast-1):end));
end
%************************************************
Ints=[];
Tms=[];
Ints= ints';
Tms= tms';
try
filterTimes= Tms; filterTimes4= Tms;
normIntens= Ints; normIntens4=Ints;
%----------------------------------------------------------------------------------------------
%classic symetric logistic curve fit setup restated as COMMENTS for reference convenience----------------------------
%opts= fitoptions is the same as for Std and so is redundant
%opts = fitoptions('Method','Nonlinear','Robust','On',...
% 'DiffMinChange',1.0E-11,'DiffMaxChange',0.001,...
% 'MaxFunEvals',me, 'MaxIter', mi, 'TolFun', 1.0E-12, 'TolX', 1.0E-10, 'Lower', [K_Guess*0.5,0,0], 'StartPoint', [K_Guess,filterTimes(floor(numTimePts/2)),0.30], 'Upper', [K_Guess*2.0,max(filterTimes),1.0]);
ftype = fittype('K / (1 + exp(-r* (t - l )))','independent','t','dependent',['K','l','r'],'options',opts);
fitObject=[]; errObj=[];
% carry out the curve fitting process
[fitObject, errObj] = fit(Tms,Ints,ftype);
coeffsArray = coeffvalues(fitObject);
r3 = coeffsArray(3); %sDat(slps,4)= coeffsArray(3); % rateS
if (exist('K','var')&& exist('r','var') && exist('l','var'))
t = (0:1:200);
GrowthELr = K ./ (1 + exp(-r.* (t - l )));
fitblELr= min(GrowthELr); %jh diag
end
catch ME
% if no data is given, return zeros
AUC = 0;MSR = 0;K = 0;r = 0;l = 0;rsquare = 0;Klow = 0;Kup = 0;
rlow = 0;rup = 0;lup = 0;llow = 0; %normIntens=[];
end %end Try
end %if stdNANcond=0
%++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
%Update values if r is better(higher) with removal of early data
try
if r3>r && stdNANcond==0
r = r3; sDat(slps,4)= sDat(slps,4); % rateS
K = coeffsArray(1); sDat(slps,2)= coeffsArray(1); % Carrying Capacity
l = coeffsArray(2); sDat(slps,3)= coeffsArray(2); %lag time
coeffsArray = coeffvalues(fitObject);
rmsStg1=errObj.rsquare;
rmsStg1I(slps)= errObj.rsquare;
sDat(slps,1)=errObj.rsquare;
%jh diagnostics*************
numFitTpts=nnz((normIntens(:)>=0)==1);
thresGT2 = find(((normIntens(:)>2)==1), 1);
thresGT2Tm = filterTimes(thresGT2);
numTptsGT2 = nnz((normIntens(:)>=2)==1);
numTimePts = length(filterTimes);
AUC = (K/r*log(1+exp(-r*(t_end-l)))-K/r*log(exp(-r*(t_end-l)))) - (K/r*log(1+exp(-r*(t_begin-l)))-K/r*log(exp(-r*(t_begin-l))));
MSR = r3;
%***************************
rsquare = errObj.rsquare;
confObj = confint(fitObject,0.9); % get the 90% confidence
NANcond=0;
confObj_filtered=confObj;
Klow = confObj(1,1); sDat(slps,5)=confObj(1,1);
Kup = confObj(2,1); sDat(slps,6)=confObj(2,1);
llow = confObj(1,2); sDat(slps,7)=confObj(1,2);
lup = confObj(2,2); sDat(slps,8)=confObj(2,2);
rlow = confObj(1,3); sDat(slps,9)=confObj(1,3);
rup = confObj(2,3); sDat(slps,10)=confObj(2,3);
if(isnan(Klow)||isnan(Kup)||isnan(llow)||isnan(lup)||isnan(rlow)||isnan(rup))
NANcond=1;
end
filterTimes= Tms;
normIntens= Ints;
resMat(17)= .00002;
resMat(18)= bl;
resMat(19)= fitblELr;
resMat(20)= minTime;
else % r is better than r3 so use the Std data in the ELr result sheet
filterTimes=selTimesStd;
normIntens=selIntensStd;
lastTptUsed= lastTptUsedStd; %Reinstall Std values for jh diags
Tpt1=filterTimes(1);
try
if isempty(Tpt1)
Tpt1= 0.00002; %777;
end
catch
Tpt1= 0.00002; %777;
end
resMat(17)= Tpt1;
numFitTpts= numFitTptsStd;
numTptsGT2= numTptsGT2Std;
thresGT2Tm = thresGT2TmStd;
cutTm(1:4)= 1000; %-1 means cuts not used or NA
resMat(18)= bl; %only applicable to Std curve Fit; ELr superceeds and makes meaningless
resMat(19)= fitblStd; %only applicable to Std curve Fit; ELr superceeds and makes meaningless
resMat(20)= minTime; %only applicable to Std curve Fit; ELr superceeds and makes meaningless
end %if r3>r1
%rup
%asdf352
% {
catch ME
% if no data is given, return zeros
AUC = 0;MSR = 0;K = 0;r = 0;l = 0;rsquare = 0;Klow = 0;Kup = 0;
rlow = 0;rup = 0;lup = 0;llow = 0; %normIntens=[];
end %end Try
%}
resMat(1)= AUC;
resMat(2)= MSR;
resMat(3)= K;
resMat(4)= r;
resMat(5)= l;
resMat(6)= rsquare;
resMat(7)= Klow;
resMat(8)= Kup;
resMat(9)= rlow;
resMat(10)= rup;
resMat(11)= llow;
resMat(12)= lup;
resMat(13)= currSpotArea;
resMat(14)= lastIntensUsed; %filtNormIntens(length(filtNormIntens));
%spline fit unneccessary and removed therfor no max spline rate time->set 0
maxRateTime=0; %ELr will show 0; Std will show []
resMat(15)= maxRateTime;
resMat(16)= lastTptUsed; %filterTimes(length(filterTimes));
try %if Std fit used no cuts .:. no cutTm
resMat(24)= cutTm(1);
resMat(25)= cutTm(2);
resMat(26)= cutTm(3);
resMat(27)= cutTm(4);
catch
resMat(24)= 999; %if Std fit used no cuts .:. no cutTm
resMat(25)= 999;
resMat(26)= 999;
resMat(27)= 999;
end
FiltTimesELr= filterTimes;
NormIntensELr= normIntens;
%**********************************************************************************
%##########################################################################
lastTptUsed=max(filterTimes);
lastIntensUsed=normIntens(length(normIntens));
if (exist('K','var')&& exist('r','var') && exist('l','var'))
t = (0:1:200);
Growth = K ./ (1 + exp(-r.* (t - l )));
fitbl= min(Growth); %jh diag
end
%}
try
if isempty(thresGT2Tm),thresGT2Tm=0;end %jh diag
catch
thresGT2Tm= 0;
numTptsGT2= 0;
end
resMat(21)= thresGT2Tm;
resMat(22)= numFitTpts;
resMat(23)= numTptsGT2;
end %function end

110
workflow/templates/easy/NCsingleDisplay.m Executable file
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%% CALLED WHEN ACCESSING 'CurveFit Display' %%
global expDir
global scLst
global ExpPath
global scan
eDir= ExpPath;
hf= figure;
%**************Parameter Entry******************
[scLst, row, col] = NCdisplayGui(eDir); %(ExpPath); %Ncode 122111replaced removed ,numOfPrtTimes)
%***********************************************
close(hf)
selSpot= (row-1)*24 + col;
for iPlate=1:length(scLst)
scanPltNum= str2double(scLst(iPlate));
%scanPltNum(iPlate);
%-----------------------------------------------------------------------
K= scan(scanPltNum).plate(1).CFout((selSpot),3);
r= scan(scanPltNum).plate(1).CFout((selSpot),4);
l= scan(scanPltNum).plate(1).CFout((selSpot),5);
suffix= strcat('Scan-Plate', scLst(iPlate)); %char(QspLst(n));
%fileSpotSuffix = strcat('-Spot#',num2str(selSpot),'-Row=',selSpotRC(1),'-Col=',selSpotRC(2),'-FitData','-L=',num2str(l),'-r=',num2str(r),'-K=',num2str(K));
fileSpotSuffix = strcat('-Spot#',num2str(selSpot),'-Row=',num2str(row),'-Col=',num2str(col),'-FitData','-L=',num2str(l),'-r=',num2str(r),'-K=',num2str(K));
filenameNoExt= [suffix fileSpotSuffix];
timeArr= scan(scanPltNum).plate(1).tSeries;
rawIntens= scan(scanPltNum).plate(1).intens((selSpot),:)/scan(scanPltNum).plate(1).Ag((selSpot));
try
filterTms= scan(scanPltNum).plate(1).filterTimes{(selSpot)};
normInts= scan(scanPltNum).plate(1).normIntens{(selSpot)};
catch
end
%********************************
if (exist('K','var')&& exist('r','var') && exist('l','var'))
t = (0:1:200);
Growth = K ./ (1 + exp(-r.* (t - l )));
end
if length(scLst)>1
figure
else
cla
end
hold on
plot(timeArr,rawIntens,'g*');
try
plot(filterTms,normInts,'o');
catch
end
hold on;
title(strcat(filenameNoExt,''));
xlabel('Hours');
ylabel('Intensities Normalized by Area');
grid on;
if (exist('K','var')&& exist('r','var') && exist('l','var'))
plot(t, Growth,'b-');
%*********Plot L on curvefit figure***********
grL=Growth(round(l)); %growthCurve timePT for l in hours
plot(l,0:grL,'-b') %to display position of l
plot(l,grL,'^b') %to display l position on curve as an arrowhead
%***Plot Arbitrary User Entry AUC "finalTimePt"
% plot(finalTimePt,0,'+m')
% plot(0:finalTimePt,bl,'-m')
end
end
%end %end for SWsingle display/plot figure
%############################################################
%Spot entry form------------------------------------------------------
%{
prompt = {'Enter spot to analyse:'};
dlg_title = 'Input spot to curve fit';
num_lines = 1;
def = {'1'};
selSpot = inputdlg(prompt,dlg_title,num_lines,def);
K= scan(scanPltNum).plate(1).CFout(str2double(selSpot),3);
r= scan(scanPltNum).plate(1).CFout(str2double(selSpot),4);
l= scan(scanPltNum).plate(1).CFout(str2double(selSpot),5);
suffix= strcat('Scan-Plate', scLst); %char(QspLst(n));
fileSpotSuffix = strcat('-Spot#',selSpot,'-FitData','-L=',num2str(l),'-r=',num2str(r),'-K=',num2str(K));
filenameNoExt= [suffix fileSpotSuffix];
timeArr= scan(scanPltNum).plate(1).tSeries;
rawIntens= scan(scanPltNum).plate(1).intens(str2double(selSpot),:)/scan(scanPltNum).plate(1).Ag(str2double(selSpot));
filterTms= scan(scanPltNum).plate(1).filterTimes{str2double(selSpot)};
normInts= scan(scanPltNum).plate(1).normIntens{str2double(selSpot)};
%}
%-----------------------------------------------------------------------
%{
prompt = {'Enter Spot row:','Enter Spot column:'};
dlg_title = 'Input spot to curve fit';
num_lines = 2;
def = {'1','1'};
selSpotRC = inputdlg(prompt,dlg_title,num_lines,def);
row= str2double(selSpotRC(1)); col=str2double(selSpotRC(2));
%}
%row= cell2mat(row);

62
workflow/templates/easy/NIcircle.m Executable file
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%% CALLED BY par4Gbl_Main8c.m %%
%{
%Imaging ToolBox method
r=14;
A=zeros(70,70); %(fIntsc(refPtR:(refPtRExt),refPtC:(refPtCExt)))
m= {40,40};
A(m{:})=1;
B= imdilate(A,strel('disk',r,0) );
imshow(B)
area=pi*r^2
clear all
%}
%without Image Proc. Toolbox
%r=14;
%A=zeros(70,70);
%A=zeros(r,r);
%P=[40,40];
%center= [refPtR+ round(.5*width), refPtC+ round(.5*width)];
%A=zeros(70,70);
%---------------------------------------------------------------------
%radius=14;
diaExt=2*(radius+1);
circBoxA=zeros(diaExt,diaExt);
center= [radius+2, radius+2];
[m, n ]=size(circBoxA);
X = bsxfun(@plus,(1:m)', zeros(1,n));
Y = bsxfun(@plus,(1:n), zeros(m,1));
cirMask= sqrt(sum(bsxfun(@minus,cat(3,X,Y),reshape(center,1,1,[])) .^2,3))<=radius;
area=pi*radius^2;
cirPixA= nnz(cirMask);
optCirMask= double(cirMask);
optCirMask(optCirMask==0)= 0.8;
%+++++++++++Foto Circle Fram(e)+++++++++++++++++++++
expansion=2;
radExpan= radius+expansion;
FdiaExt=2*(radExpan);
circBoxA=zeros(FdiaExt,FdiaExt);
center= [radExpan+1, radExpan+1];
[m, n ]=size(circBoxA);
X = bsxfun(@plus,(1:m)', zeros(1,n));
Y = bsxfun(@plus,(1:n), zeros(m,1));
FcirMask= sqrt(sum(bsxfun(@minus,cat(3,X,Y),reshape(center,1,1,[])) .^2,3))<=radExpan;
%FcirPixA= nnz(cirMask);
FoptCirMask= double(FcirMask);
FoptCirMask(FoptCirMask==1)= 2;
%FoptCirMask(FoptCirMask==0)= 1;
%********Combine Masks to create circular boundry************
padOptCirMask= padarray(optCirMask,[expansion-1 expansion-1],0.8);
FoptCirMask= FoptCirMask .* padOptCirMask;
FoptCirMask(FoptCirMask==1.6)= 0.8;
FoptCirMask(FoptCirMask==0)= 1;
FoptCirMask(FoptCirMask==2)= 1;
%---------------------------------------------------
%imagesc(cirMask)

281
workflow/templates/easy/NImParamRadiusGui.m Executable file
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%% CALLED BY par4Gbl_Main8c.m %%
function NImParamRadiusGui(expDir) %, numOfPrtTimes) 122111replace removed
global SWsingleSc
global SWgrowthArea
%global selScan
global scan
global scLst
global ImParMat
%global CSearchRange
global CSrchRng
global defImParMat
global fhImRun
global fhconsole
global resDir
global ExpOutmat
global numRows;
global numCols;
global scanSize
global scanMax
defImParMat=[1, 1, 15, 34, 24, 1,0,0,1,14,1,18]; %Ncode ImRobot adaptation
if ImParMat(3)==0 || ImParMat(4)==0 ||ImParMat(5)==0 || ImParMat(10)==0 ||ImParMat(11)==0
ImParMat=defImParMat;
end
if size(ImParMat,2)<12
ImParMat(12)=18; %Default before user input CsearchRange value
msg= 'Data made before SearchRange user entry added (ImParMat(12). 18 was the set value and the current default.)';
end
%ImParMat=defImParMat; %Activate for INITIAL USE only
MPnum=1;
destPerMP=1;
selScan=1;
SWgrowthArea=1;
if exist(fullfile(resDir,'PTmats','NImParameters.mat'))
load(fullfile(resDir,'PTmats','NImParameters'));
else
load NImParameters
end
ImParMat;
%end
%if ~exist('CSearchRange','var') || isempty(CSearchRange)
if ~isequal(exist(fullfile(resDir,'Fotos','CSearchRange.mat')),0)
load(fullfile(resDir,'Fotos','CSearchRange'))
CSearchRange;
end
% yInitPos=0.30;
xPos=0.05;
btnWid=0.10;
btnHt=0.05;
spacing=0.02;% Spacing between the button and the next command's label
%====================================
% The ADD Groups button
btnNumber=1;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
fhImParm=gcf;
if exist('resDir','var')&& ~isempty(resDir)
set(fhImParm,'NumberTitle','off')
set(fhImParm,'Name',strcat('ImageAnalysis- ',char(resDir)))
else
set(fhImParm,'NumberTitle','off')
set(fhImParm,'Name','EASYconsole -Exp. Analysis NOT selected.')
end
btnNumber=5;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
srcRadius=ImParMat(10);
hedit = uicontrol(...
'Style', 'edit',...
'String',srcRadius,...
'Units','normalized',...
'Position', btnPos,... % [.002 .70 .08 .10],...
'callback',{@entryRadius}); % 'Position', [5 100 60 20])
function entryRadius(source,~)
user_entry = str2double(get(source,'string'));
if (isnan(user_entry)||(user_entry<12)||(user_entry>17))
errordlg('You must enter a numeric value between 12 and 17','Bad Input','modal')
return
end
Radius=user_entry;
ImParMat(10)= Radius;
Radius;
end
btnNumber=6;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
srcDither= ImParMat(6);
hedit = uicontrol(...
'Style', 'edit',...
'String',srcDither,...
'Units','normalized',...
'Position', btnPos,...
'callback',{@entryDither});
function entryDither(source,~)
user_entry = str2double(get(source,'string'));
if (isnan(user_entry)||(user_entry<0)||(user_entry>5))
errordlg('You must enter a numeric value between 1 and 4','Bad Input','modal')
return
end
Dither=user_entry;
ImParMat(6)= Dither;
Dither;
end
%-------------------77777----------- Added July 7,2015 to allow Search Range constraint
btnNumber=7;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
try
CSrchRange=ImParMat(12);
CSrchRng=ImParMat(12);
catch %Legacy default value was 18 before being made a user input variable (ImParMat(12)). A preferable value now might be 12 or 14.
CSrchRange=18;
ImParMat(12)=18;
CSrchRng=ImParMat(12);
end
hSearchRange = uicontrol(...
'Style', 'edit',...
'String',CSrchRange,...
'Units','normalized',...
'Position', btnPos,...
'callback',{@CsearchRange});
function CsearchRange(source,~)
user_entry = str2double(get(source,'string'));
if (isnan(user_entry)||(user_entry<1)||(user_entry>50)) %originally 18; 19_0729 increased
errordlg('You must enter a numeric value between 1 and 18 12->18 recommended. (ImParMat(12)))','Bad Input','modal')
return
end
CSrchRng=user_entry;
end
%Ncode 12_0120 for reading in numeric folder names
nlist=dir(fullfile(expDir,'*'));
nnn=0;
for n=1:size(nlist,1)
if (~isempty(str2num(nlist(n).name)))
nnn=nnn+1;
PnumLst(nnn)= (str2num(nlist(n).name));
sl(nnn,1)={(nlist(n).name)};
end
end
scanSize= size(sl,1);
scanMax= max(str2double(sl));
hListbox = uicontrol(...
'Style', 'listbox',...
'String',sort(sl),...
'value',[],...
'max',1000,...
'min',1,...
'Units','normalized',...
'Position', [.70 .40 .10 .60],...
'callback',{@load_listbox}); %'uiresume(gcbf)'); 'Position', [5 100 60 20])
function load_listbox(source,~)
%global CSrchRng
%global CSrearchRange
userIndx = (get(source,'value'));
userStr = (get(source,'string'));
%scLstIndx= str2num(char(strrep(userStr(userIndx), 'Scan', '')))
user_entry=userStr(userIndx);
scLst=user_entry;
if size(scLst,1)>1
%CSrchRng=num2str(ImParMat(12))
set(hSearchRange,'string',num2str(ImParMat(12)))
else
try
CSrchRng=CSearchRange(str2double(scLst));
set(hSearchRange,'string',CSearchRange(str2double(scLst)))
catch
% CSrchRng=num2str(ImParMat(12))
% set(hSearchRange,'string',num2str(ImParMat(12)))
end
end
%ImParMat(7)=MPnum
end
scLst;
%*****************************************************************
%-------------------10 10 10 10-----------
btnNumber=10;
yPos=0.85-(btnNumber-1)*(btnHt+spacing);
btnPos=[xPos yPos-spacing btnWid btnHt];
hedit8 = uicontrol(...
'Style', 'pushbutton',...
'String',{'Continue'},...
'Units','normalized',...
'Position', btnPos,...
'callback','uiresume(gcbf)');
%------------------------------
%***************************************************************
%********LABELS******************************
% The Labels
xLPos=0.175;
yPos=0;
btnWid=0.20;
%-------------------55555-----------
lblNumber=5;
yPos=0.85-(lblNumber-1)*(btnHt+spacing);
btnPos=[xLPos yPos-spacing btnWid btnHt];
htxt = uicontrol(...
'Style', 'text',...
'String','Radius',... %'String','Width',...
'Units','normalized',...
'Position', btnPos);
%-------------------66666-----------
lblNumber=6;
yPos=0.85-(lblNumber-1)*(btnHt+spacing);
btnPos=[xLPos yPos-spacing btnWid btnHt];
htxt = uicontrol(...
'Style', 'text',...
'String','Dither',...
'Units','normalized',...
'Position', btnPos);
%-------------------77777-----------
lblNumber=7;
yPos=0.85-(lblNumber-1)*(btnHt+spacing);
btnPos=[xLPos yPos-spacing btnWid btnHt];
htxt = uicontrol(...
'Style', 'text',...
'String','SearchRange',...
'Units','normalized',...
'Position', btnPos);
uiwait(gcf);
for i=1:length(scLst)
CSearchRange(str2double(scLst(i)))= CSrchRng;
ImParMat(12)= CSrchRng;
end
ImParMat;
CSearchRange;
try
save('NImParameters','ImParMat')
% save('CSearchRange','CSearchRange')
catch
save(fullfile('\','NImParameters'),'ImParMat')
%save(fullfile('\','CSearchRange'),'CSearchRange')
end
save((fullfile(resDir,'PTmats','NImParameters')), 'ImParMat');
save((fullfile(resDir,'Fotos','CSearchRange')),'CSearchRange');
close
return
end

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workflow/templates/easy/NIscanIntensBGpar4GblFnc.m Executable file
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workflow/templates/easy/datatipp.m Executable file
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%% PART OF GUI FUNCTIONALITY %%
function output_txt = datatipp(~,event_obj)
% Display the position of the data cursor
% obj Currently not used (empty)
% event_obj Handle to event object
% output_txt Data cursor text string (string or cell array of strings).
pos = get(event_obj,'Position');
output_txt = {['X: ',num2str(pos(1),4)],...
['Y: ',num2str(pos(2),4)]};
% If there is a Z-coordinate in the position, display it as well
if length(pos) > 2
output_txt{end+1} = ['Z: ',num2str(pos(3),4)];
end

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workflow/templates/easy/p4loop8c.m Executable file
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%% CALLED BY par4Gbl_Main8c.m %%
function[p4L4,...
TmpexpScanIntens4,TmpFexpScanSpots4,TmpFexpScanBMtp4,TmpanlZoneRefs4,Tmpsbdg4]= ...
p4loop8c(parMat,tptLength,numScans,selScanNumLst,SWsingleSc,Fflg,PTmapPos,optCirMask,diaExt,doCircle,cirPixA,cirMask,width, ...
TmpexpScanIntens00,TmpFexpScanSpots00,TmpFexpScanBMtp00,TmpanlZoneRefs00,~,tifFileLstP4,pathname,ImParMat, ...
numRows,numCols,scLst,resDir,expDir, p4L00,TmpexpScanIntens4,TmpFexpScanSpots4,TmpFexpScanBMtp4,TmpanlZoneRefs4, Tmpsbdg00, Tmpsbdg4)
p4L0=p4L00;
TmpexpScanIntens0= TmpexpScanIntens00;
TmpFexpScanSpots0= TmpFexpScanSpots00;
TmpFexpScanBMtp0= TmpFexpScanBMtp00;
TmpanlZoneRefs0= TmpanlZoneRefs00;
Tmpsbdg0= Tmpsbdg00;
%resDir %for debugging
%START PARFOR PARFOR PARFOR PARFOR PARFOR PARFOR PARFOR PARFOR PARFOR PARFOR
%************************************************************************************************************************
%---------------Global Parfor Loop-----------------------------------------
%for scCount=1:numScans
if SWsingleSc==1
parforArg=0;
else
parforArg= inf;
end
%for (scCount=1:numScans)
parfor (scCount=1:numScans,parforArg)
scCount %for debugging
p4L0= cell(18,1);
[p4L3,...
TmpexpScanIntens3,TmpFexpScanSpots3,TmpFexpScanBMtp3,TmpanlZoneRefs3,Tmpsbdg3]= ...
par4GblFnc8c(parMat,tptLength,numScans,selScanNumLst,SWsingleSc,Fflg,PTmapPos,optCirMask,diaExt,doCircle,cirPixA,cirMask,width, ...
TmpexpScanIntens0,TmpFexpScanSpots0,TmpFexpScanBMtp0,TmpanlZoneRefs0,scCount,tifFileLstP4,pathname,ImParMat, ...
numRows,numCols, scLst,resDir,expDir, p4L0,Tmpsbdg0);
p4L4(:,scCount)= p4L3; %(:,scCount);
TmpexpScanIntens4(scCount)= TmpexpScanIntens3;
TmpFexpScanSpots4(scCount)= TmpFexpScanSpots3;
TmpFexpScanBMtp4(scCount)= TmpFexpScanBMtp3;
TmpanlZoneRefs4(scCount)= TmpanlZoneRefs3;
Tmpsbdg4(scCount)= Tmpsbdg3;
%End of Global Scan loop*******************************************************************************************
%**************************************************************************************************************************
end
%---------------END OF Global Parfor Loop-----------------------------------------%**************************************************************************************************************************

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workflow/templates/easy/par4GblFnc8c.m Executable file
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%% CALLED By p4loop8c.m %%
function [p4L2, ...
TmpexpScanIntens3,TmpFexpScanSpots3,TmpFexpScanBMtp3,TmpanlZoneRefs3,Tmpsbdg3]= ...
par4GblFnc8c(parMat,tptLength,~,selScanNumLst,~,Fflg,PTmapPos,optCirMask,diaExt,doCircle,cirPixA,cirMask,~,...
TmpexpScanIntens,TmpFexpScanSpots,TmpFexpScanBMtp,TmpanlZoneRefs,scCount,tifFileLstP4,~,ImParMat, ...
numRows,numCols,scLst,resDir,expDir,~, Tmpsbdg)
selScan= selScanNumLst(scCount);
tptLength0= length(tifFileLstP4{scCount});
%tptLength= numFiles;
tifFileLst={tifFileLstP4(scCount)};
% Extract the Imaging time stamps from selected tif files
%clear('e','f'); %can't use clear inside a parfor loop. Preallocation
%can be larger than useable .bmp files! Therefore must be small and
%increased during for loop to maintain cell size integrity between e & f
e= cell(1,2); f= cell(1,2); %(tptLength,2); f= cell(tptLength,2);
nndx=0;
for tPt=1:tptLength0 %size(tifFileLst,1) %length(tifFileLst)
tifFileLstP4{scCount}(tPt)
scLst;
scLst(scCount)
char(scLst(scCount))
char(fullfile(expDir,char(scLst(scCount))))
expDir;
swCatch=0;
nndx=nndx+1;
tifFile=char(fullfile(expDir,char(scLst(scCount)), tifFileLstP4{scCount}(tPt)));
try
info = imfinfo(tifFile); %('D:\jwrDevel\DevelCurveFittingJWR\ImageScans\Scan2\020hr002.tif')
catch ME
%Note: During parallel operation Matlab will not open file (fid)
%etc. Therefore error message text will not be written.The only way
%to get it out would be to pass variable through called function to
%the ..Main8c script outside the parfor loop and print to file from
%there. Consequently for now it only prints error to file when one
%edits p4loop8c.m from 'parfor' to ordinary 'for' loop
fFail=((fullfile(resDir,'PrintResults','ImageFileReadFailure.txt')));
fid = fopen(fFail,'a'); %create,open and append
%fprintf(fid,'%s \n',char(tifFile))
fclose(fid)
nndx=nndx-1;
swCatch=1;
rep = getReport(ME, 'basic');
rep=strcat('Read info failure for-',tifFile,' -', rep);
%fprintf(fid,'%s \n',rep) %See Note:
end
tptLength= nndx;
scTmNumeric= 1; %initialize for parfor
if swCatch==0
scTmNumeric(nndx)=datenum(info.FileModDate);
e(nndx,:)= {tifFile, scTmNumeric(nndx)};
%newtifFileLst(nndx)= tifFileLst(tPt);
end
end % end for tPt=1:length(tifFileLst) loop
%clear tifFileLst; %Can't use clear inside a parfor loop
tifFileLst= cell(nndx,1);
f= {sortrows(e,2)};
tifFileLst= f{1,1}(:,1);
areaOfIntensAboveBG= zeros(24,16,length(tifFileLst));
% *******Calculate Time series for each Plate of Selected Scan ********
lastPlateOnScan=1; %Ncode
tSeriesv=[]; t0Seriesv=[];
if tptLength>0 %added to jump over and fill data for invalid Sscan(plate runs
scTmNumv= cell2mat(f{1,1}(:,2)); %(:,2)) %120613 fix for variant length data
prtTmNumv=min(scTmNumv)-.000001;
tSeriesv=((scTmNumv-prtTmNumv)*24);
t0Seriesv=((scTmNumv-scTmNumv(1))*24);
end
%*********************
%-------------------------------------------------------
if tptLength>= 3 %added to jump over and fill data for invalid Sscan(plate runs
%*******Create Blank Scan*********************
ImHeigth=2075;
ImWidth=1400;
Empsc=zeros(ImHeigth,ImWidth); %Ncode
%**************************************************************************
%*********Start Scan Loop**************************************************
lastPlateOnScan=1; %Ncode
%**********************************************************************************************************************************
disp('Before call to NIscanIntens.....')
resDir; %debugging parfor
%>>>*******Execute Image conversion into Intensity Data******
[Tmpsbdg2, scanIntens, ~, ~, ~, TmpexpScanIntens2, TmpFexpScanSpots2, TmpFexpScanBMtp2, TmpanlZoneRefs2,areaOfIntensAboveBG]= ...
NIscanIntensBGpar4GblFnc(Fflg,tifFileLst, ImParMat, PTmapPos,optCirMask,diaExt,doCircle,cirPixA,numRows,numCols,ImHeigth,ImWidth,cirMask, ...
tptLength,selScan,Empsc,TmpexpScanIntens,TmpFexpScanSpots,TmpFexpScanBMtp,TmpanlZoneRefs,resDir, Tmpsbdg);
%<<<<*******************************************************************************************************************************
TmpexpScanIntens3= TmpexpScanIntens2;
TmpFexpScanSpots3= TmpFexpScanSpots2;
TmpFexpScanBMtp3= TmpFexpScanBMtp2;
TmpanlZoneRefs3= TmpanlZoneRefs2;
Tmpsbdg3= Tmpsbdg2;
%***********************************************************************************
%Package Image data ->for Legacy Printing
%clear plate %Can't use clear inside a parfor loop
CFscanIntens= zeros(384,1);%zeros(16,24);
plate= [];
plate= zeros(24,16,tptLength);
plate(:,:,:,1)= scanIntens(1:1:24,16:-1:1,:); %TmpexpScanIntens2(1:1:24,16:-1:1,:);%Ncode Dev3Vertical Similar to below
%*******************************
%NIcheck %Check for bad scans at time points (swapped plates etc.)
%*******************************
%set up cell arrays for storing each plate in each Scan ..(scan,plate)
SWprint=0;
if SWprint==1
wkDir=pwd;
cd (fullfile(resDir,'PrintResults'));
end
% Construct Legacy ...Intens.txt file
if SWprint==1
filename=(strcat('Plate',num2str(selScan),'_Intens.txt'));
fid = fopen(filename,'w');
end
if length(size(plate))==2 %Only two dims if only one image
numOfImages=1;
else
numOfImages= size(plate,3);
end
CFscanIntens= zeros(384,numOfImages);
locIndx=0; pl=1;
for n=1:numCols %Ncode changed to 16 for Vert
for m=1:numRows %Ncode change to 24 for Vert
locIndx=locIndx+1;
for k=1:numOfImages
if SWprint==1
if k==1 && numOfImages==1, fprintf(fid,'%.2f\n',plate(m,n,k,pl));end
if k==1 && numOfImages~=1, fprintf(fid,'%.2f',plate(m,n,k,pl));end
if k>1 && k<numOfImages, fprintf(fid,'\t%.2f',plate(m,n,k,pl));end %
if k~=1 && k==numOfImages,fprintf(fid,'\t%.2f\n',plate(m,n,k,pl));end
end
CFscanIntens(locIndx,k)= plate(m,n,k,pl);
end
%MatLab Cell storage
end
end %end row loop n
if SWprint==1
fclose(fid);
end
%++++++++++++++++++++++
%printGrwAreas
%Area as the max number of pixels with intensities greater than the Background
%grArea(row,col,tPt,Plate) Note that images r and c are 90 degrees shifted
%and then mirror imaged. Thus data must be inverted and rotated to get
%for the rows a-p and col 1-24 (and the EMS expected 1-384) orientation
%clear grArea
grArea= ones(24,16,tptLength);
grArea(:,:,:,1)= areaOfIntensAboveBG(1:1:24,16:-1:1,:); %for Ncode dev3vert
%for p=1:lastPlateOnScan
if SWprint==1
if SWgrowthArea==1
filename=(strcat('Plate',num2str(selScan),'_Areas.txt'));
else
filename=(strcat('ALTgrowthA_Scan',num2str(selScan),'_Plate',num2str(1),'_Areas.txt'));
filename=(strcat('ALTgrowthA_Plate',num2str(selScan),'_Plate','_Areas.txt'));
end
fid = fopen(filename,'w');
end
locIndx=0;
Ag= zeros(1,384);
for m=1:16 %Ncode change from 16 %Vert back to 16
for n=1:24 %Ncode change from 24 %Vert back to 24
growthArea=max(grArea(n,m,:,1));
if SWprint==1
fprintf(fid,'%3.f\n',growthArea);
end
locIndx=locIndx+1;
Ag(locIndx)= growthArea;
end
end
if SWprint==1
fclose(fid);
end
%end
%++++++++++++++++++++++++
if SWprint==1
cd(wkDir);
fclose('all');
end
%********AutoImCF curveFit kickoff setup***********************************************************
autoImCFlag=1;
if autoImCFlag==1, SWgrowthArea=1;end
times= tSeriesv;
scanAreas= Ag; %growthArea;
offsets=0;
suffix= strcat('Scan', num2str(selScan),'_Plate', num2str(1)); %char(QspLst(n));
AUCfinalTime=96;
arrayFormat=384;
currDirResults= fullfile(resDir,'PrintResults');
%******Version compatability fixes*******assoc'd with diff and solve
%{
v11a='7.12.0.635 (R2011a)';
v14a='8.3.0.532 (R2014a)';
%v14b='8.4.0.150421 (R2014b)';
v18a='9.4.0.813654 (R2018a)';
v18b='9.5.0.944444 (R2018b)';
%Fourth order derivative of logistic equation********************************
if isequal(v18a,version)||isequal(v18b,version)
syms t K r l;
fd4= diff(K / (1 + exp(-r* (t - l ))),t,4);
else
fd4=diff(sym('K / (1 + exp(-r* (t - l )))'),4);
end
sols= solve(fd4);
if isequal(v11a,version) || isequal(v14a,version)
else
tmpswap= sols(1);
sols(1)= sols(3);
sols(3)= tmpswap;
end
%}
if verLessThan('matlab','8.3') %original work 23_0227 updated 23_0525 (8.4 changed to 8.3)
fd4=diff(sym('K / (1 + exp(-r* (t - l )))'),4);
sols= solve(fd4);
else %accomodate new matlab changes after 2014a fix 2nd update 23_0227
syms t K r l;
fd4= diff(K / (1 + exp(-r* (t - l ))),t,4);
sols= solve(fd4);
tmpswap= sols(1);
sols(1)= sols(3);
sols(3)= tmpswap;
end
%********************************************************************************
%CFscanIntens
%adsd
%********************************************************************************
%>>>>>>>>>>>Call CurveFit routine >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
%NCfitImCF(times, CFscanIntens, offsets, suffix, AUCfinalTime, arrayFormat, scanAreas, currDirResults, autoImCFlag, selScan,sols) %,scan)%, scPltList) outputDirectory;
%[scanTmp2]= NCfitImCFparforFailGbl(times, CFscanIntens, offsets, suffix, AUCfinalTime, arrayFormat, scanAreas, currDirResults, autoImCFlag, selScan, sols, scanTmp); %,scan)%, scPltList) outputDirectory;
[par4scanselIntensStd,par4scanselTimesStd,par4scanTimesELr,par4scanIntensELr,par4scanCFparameters,par4scanCFdate,outC2,outCstd2]= ...
NCfitImCFparforFailGbl2(parMat,times, CFscanIntens, offsets, suffix, AUCfinalTime, arrayFormat, scanAreas, currDirResults, autoImCFlag, selScan, sols); %,scan)%, scPltList) outputDirectory;
%<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
else %fill with default values when an invalid plate scan occurs
CFscanIntens= zeros(16,24);
Ag= zeros(1,384);
%Preallocation for parfor loop**********************************
times= tSeriesv;
st(1,1:size(times,2))= 1111;
resMat(1,1:27)= 0;
resMatStd= resMat;
outC2= zeros(384,27);
outCstd2= zeros(384,27);
for m=1:384
pa{m}= st;
par4scanCFparameters{m}= parMat;
par4scanCFdate{m}= datestr((now),31);
end
par4scanselTimesStd= pa;
par4scanselIntensStd= pa;
par4scanTimesELr= pa;
par4scanIntensELr= pa;
par4resMat= zeros(384,27);
par4resMatStd= zeros(384,27);
%{
TmpexpScanIntens00= cell(1); %cell(1,scanMax);
TmpFexpScanSpots00= cell(1); %cell(1,scanMax);
TmpFexpScanBMtp00= cell(1); %cell(1,scanMax);
TmpanlZoneRefs00= cell(1); %cell(1,scanMax);
Tmpsbdg00= cell(1);
%}
TmpexpScanIntens3= cell(1); %TmpexpScanIntens2;
TmpFexpScanSpots3= cell(1); %TmpFexpScanSpots2;
TmpFexpScanBMtp3= cell(1); %TmpFexpScanBMtp2;
TmpanlZoneRefs3= cell(1); %TmpanlZoneRefs2;
Tmpsbdg3= cell(1); %Tmpsbdg2;
%****************************************************************
end %if tptLenth>=3 line19 20_0928
tSeriesv; %debuggin parfor
p4L1{1}= tSeriesv;
p4L1{2}= t0Seriesv;
p4L1{3}= datestr(prtTmNumv,31);
p4L1{4}= CFscanIntens;
locIndx=0;
for n=1:numCols %Ncode changed to 16 for Vert
for m=1:numRows %Ncode change to 24 for Vert
locIndx=locIndx+1;
rc=[n,m];
p4rcTmp(locIndx)={rc};
p4pIndxTmp(locIndx)=locIndx;
end
end
p4L1{5}= p4rcTmp;
p4L1{6}= p4pIndxTmp;
p4L1{7}= Ag;
p4L1{8}= par4scanselIntensStd;
p4L1{9}= par4scanselTimesStd;
p4L1{10}= par4scanTimesELr;
p4L1{11}= par4scanIntensELr;
p4L1{12}= par4scanCFparameters;
p4L1{13}= par4scanCFdate;
p4L1{14}= outC2;
p4L1{15}= outCstd2;
p4L1{16}= selScan;
p4L1{17}= cirPixA;
p4L1{18}= datestr((now),31);
p4L2= p4L1;
end

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%% CALLED BY EASYconsole.m %%
%function NImStartupImCF02par4Gbl
Fflg= 1; %0;
fclose('all'); %close all open files
clear ('plate2', 'scanIntens','Scanfiles','pathname','tifFileLstP4')
%global SWsingleSc
global SWgrowthArea
global scLst
global ImParMat
%global CSearchRange
%global CSrchRng
global expDir
global SWnewExp
%Console globals*******
global openExpfile
global openExppath
global newExpfile
global newExppath
global ExpOutmat
global fhconsole
global ExpPath
global resDir
global wCodeDir
global matDir %
global ImWidth
global ImHeigth
global numRows;
global numCols;
%global SWprintLeg
global scan
%global scanSize
global scanMax
global tptLength
%global sols
%global CFmeth
numRows=24; %for Single Vertical
numCols=16; %for Single Vertical
%global scanPar4x
%*************CIRCLE related*************************
doCircle=1; %use Circle area analysis 14_0807
radius=14;
ImParMat(10)=radius;
ImParMat(11)=doCircle;
try
clf(fhconsole,'reset')
catch ME
end
close
%******************************************
EASYconsole
%******************************************
try
load(ExpOutmat)
copyfile(ExpOutmat,(fullfile(matDir,'BkUp',strcat((num2str(datenum(now))),'.mat'))))
catch
end
try
load(fullfile(resDir,'Fotos','Nbdg')) %Modified to load from 'Fotos' 20_0819
catch
%Reloacated from 'PTmats' to prevent potential overwrite when PTmats is
%copied into new job when the PT template is about the same. We also
%now have a default template if one is not made. i.e., when the images
%from the new experiment are too sketchy to make a good pintool
%template. By moving it to 'Fotos' we avoid possible issues due to
%copying the Nbdg.mat file along with the default template '.mat' files.
%A copy of Ndbg.mat is placed also saved to the 'PTmats' directory
%after each run to allow previous version of EASY to access data made
%by EASY versions after 20_0819.
load(fullfile(resDir,'PTmats','Nbdg')) %Left in to accomodate loads of work before 20_0819
end
%++++++++++++++Load Fotos stored data++++++++++++++++++++
try
load(fullfile(resDir,'Fotos','Coordinates'))
catch
end
try
load(fullfile(resDir,'Fotos','BGatTpts'))
catch
end
try
load(fullfile(resDir,'Fotos','anlZones'))
catch
end
%******autoImCF*******************
try
load(fullfile(resDir,'PTmats','NCFparms'))
catch ME
load parameters
end
%*******************************
%************Get Print Times*******************************
PrintTimes=[];
w= cd; %Capture current dir in w
if ispc %Linux accommodation
expDir=fullfile(ExpPath,'\');
else
if isunix, expDir= ExpPath;end
if ismac , expDir=ExpPath;end
end
scLst={};
%**************Parameter Entry******************
NImParamRadiusGui(expDir) %Ncode 122111replaced removed ,numOfPrtTimes)
%***********************************************
%width=ImParMat(5);
width=24;
widthEx=width-1; %width extention from reference point
dither=ImParMat(6);
radius=ImParMat(10);
%>>>>>>>>>>>>>>>>>>>>>>
NIcircle
%<<<<<<<<<<<<<<<<<<<<<<<
%***************** Load Stuff*************************
lastPlateOnLastScan=1; %Ncode
if size(scLst,1)==1,SWsingleSc=1;else SWsingleSc=0;end
%**************************????????????????????????
dvec=datevec(datestr(floor(now))); %method to get current offset year '01-Jan-"currentyr"'
dvec(2)=1;
dvec(3)=1;
%yrOffset=datenum('01-Jan-2012');%(dvec); %('01-Jan-2009'); %time num default is currentyear jan1
%******************+++++++++++++*****************+++++++++++++++***********
numScans=size(scLst,1);
if(isequal(SWsingleSc,1))
selScan=str2double(char(scLst(1)));
%numScans=selScan;
%startScan=selScan;
else
%startScan=1;
end
SWgrowthArea= ImParMat(9);
load(fullfile(resDir,'PTmats','NPTmapSearch'))
PTmapPos= detPos;
%**************************************************************************
selScanNumLst= [];
%++++++++++++++++++++++++++++++++++++++++++++++++++++++++
%**************************************************************************
%*********Preallocation for Scan Loop**************************************************
Scanfiles=[];
pathname=[];
%++++++++++++++++++++++++++++++++ SETUP FOR GLOBAL PARFOR LOOP+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
%if SWsingleSc == 1 %if single scan else do expMultiTseries to execute multiple scans
%******Gui Select Scan -> *.tif files for Analysis*****************
w= cd; %Capture current dir in w
if ispc
cd(char(strcat(expDir,scLst(1))))
end
if isunix
cd (fullfile(expDir,cell2mat(scLst(1))));
end
Scanfiles=[];
pathname=[];
for ii= 1:length(scLst)
if SWsingleSc == 1
[Scanfiles, pathname]=uigetfile('*.bmp', 'Select files','MultiSelect','on');% change '*hr*.bmp' 12/20/2011
if ischar(Scanfiles)
scd= imread(char(Scanfiles));
tptLength=1;
else
scd= imread(char(Scanfiles(1,1)));
tptLength= length(Scanfiles);
end
ImHeigth= size(scd,1);
ImWidth= size(scd,2);
sc=scd(1:ImHeigth,1:ImWidth); %?Not used RefOnly
end
cd (w);
numFiles= size(Scanfiles,2);
%tifFileLst= Scanfiles;
%Initialize tifFilesLst for parfor loop
if ispc %Linux and mac accomodation
tifFileLst4MultiT = dir(fullfile(expDir, char(scLst(ii)), '\*.bmp'));
end
if isunix || ismac
tifFileLst4MultiT = dir(fullfile(expDir, char(scLst(ii)), '*.bmp'));
end
numFiles=length(tifFileLst4MultiT);
tptLength= numFiles;
tifFileLstP4{ii}={tifFileLst4MultiT.name};
%{
dateTmStampP4{ii}= {tifFileLst4MultiT.date}
dateTmNum{ii}= datenum(dateTmStampP4{1});
info{ii} = imfinfo(tifFileLstP4{ii});
scTmNumericP4(ii)=datenum(info{ii}.FileModDate);
%}
end
%**************************************************************************
%**************************************************************************
for jj= 1:numScans %startScan:numScans
selScan= str2double(char(scLst(jj)));
selScanNumLst(jj)= selScan;
end
selScanNumLst2= selScanNumLst; %function passthrough, passback to par4gbl_Main 20_0205
%++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
%PREALLOCATION PREALLOCATION PREALLOCATION PREALLOCATION PREALLOCATION
%******************************************************************************
scCount= [];
TmpexpScanIntens00= cell(1); %cell(1,scanMax);
TmpFexpScanSpots00= cell(1); %cell(1,scanMax);
TmpFexpScanBMtp00= cell(1); %cell(1,scanMax);
TmpanlZoneRefs00= cell(1); %cell(1,scanMax);
Tmpsbdg00= cell(1);
TmpexpScanIntens4= cell(1,numScans);
TmpFexpScanSpots4= cell(1,numScans);
TmpFexpScanBMtp4= cell(1,numScans);
TmpanlZoneRefs4= cell(1,numScans);
Tmpsbdg4= cell(1,numScans);
TmpexpScanIntens5= cell(1,numScans);
TmpFexpScanSpots5= cell(1,numScans);
TmpFexpScanBMtp5= cell(1,numScans);
TmpanlZoneRefs5= cell(1,numScans);
Tmpsbdg5= cell(1,numScans);
p4L00= cell(18,1);
p4L0= p4L00;
p4L4= cell(18,numScans);
p4L5= p4L4;
Ag= ones(384);
CFscanIntens= zeros(16,24);
[p4L4,...
TmpexpScanIntens5,TmpFexpScanSpots5,TmpFexpScanBMtp5,TmpanlZoneRefs5,Tmpsbdg5]= ...
p4loop8c(parMat,tptLength,numScans,selScanNumLst,SWsingleSc,Fflg,PTmapPos,optCirMask,diaExt,doCircle,cirPixA,cirMask,width, ...
TmpexpScanIntens00,TmpFexpScanSpots00,TmpFexpScanBMtp00,TmpanlZoneRefs00,scCount,tifFileLstP4,pathname,ImParMat, ...
numRows,numCols,scLst,resDir,expDir, p4L00,TmpexpScanIntens4,TmpFexpScanSpots4,TmpFexpScanBMtp4,TmpanlZoneRefs4, ...
Tmpsbdg00,Tmpsbdg4);
for scanCnt= 1:numScans
selScan= p4L4{16,scanCnt}; %determine the actual scan in the scanCnt parfor distributed "id"
scan(selScan).plate(1).tSeries= cell2mat(p4L4(1,scanCnt));
scan(selScan).plate(1).t0Series= cell2mat(p4L4(2,scanCnt));
scan(selScan).plate(1).printTm= cell2mat(p4L4(3,scanCnt));
scan(selScan).plate(1).intens= cell2mat(p4L4(4,scanCnt));
scan(selScan).plate(1).rc= p4L4(5,scanCnt);
scan(selScan).plate(1).pIndx= cell2mat(p4L4(6,scanCnt));
scan(selScan).plate(1).Ag= cell2mat(p4L4(7,scanCnt));
scan(selScan).plate(1).selIntens= p4L4(8,scanCnt);
scan(selScan).plate(1).selTimes= p4L4(9,scanCnt);
scan(selScan).plate(1).filterTimes= p4L4(10,scanCnt);
scan(selScan).plate(1).normIntens= p4L4(11,scanCnt);
%scan(selScan).plate(1).CFparameters= p4L4(12,scanCnt); %Need to convert to a matrix form like Old versions
CFparm(1:384)=p4L4{12,scanCnt}(1:384);
scan(selScan).plate(1).CFparameters= CFparm;
scan(selScan).plate(1).CFdate= p4L4(13,scanCnt);
scan(selScan).plate(1).CFout= cell2mat(p4L4(14,scanCnt));
scan(selScan).plate(1).CFoutStd= cell2mat(p4L4(15,scanCnt));
scan(selScan).Awindow= cell2mat(p4L4(17,scanCnt));
scan(selScan).Idate= cell2mat(p4L4(18,scanCnt));
expScanIntens(selScan)= TmpexpScanIntens5(scanCnt);
FexpScanSpots(selScan)= TmpFexpScanSpots5(scanCnt);
FexpScanBMtp(selScan)= TmpFexpScanBMtp5(scanCnt);
anlZoneRefs(selScan)= TmpanlZoneRefs5(scanCnt);
if ~isempty(Tmpsbdg5{scanCnt})
sbdg(selScan)= Tmpsbdg5(scanCnt);
else
sbdg{selScan}= uint8(zeros(24,16,4));
end
end
%SAVE DATA in .mat files
save(ExpOutmat,'scan');
save((fullfile(resDir,'PTmats','Nbdg')), 'sbdg'); %legacy location can probably get rid of in time
save((fullfile(resDir,'Fotos','Nbdg')), 'sbdg');
save((fullfile(resDir,'Fotos','Coordinates')),'FexpScanSpots') %Saves frames at each tPt
save((fullfile(resDir,'Fotos','BGatTpts')),'FexpScanBMtp')
save((fullfile(resDir,'Fotos','anlZones')),'anlZoneRefs')%Saves anl Positions at each tPt
%Print FitResults *******************************************************
fileExt = '.txt';
filePrefix = 'FitResults_';
for scanCnt= 1:numScans
selScan= p4L4{16,scanCnt}; %determine the actual scan in the scanCnt parfor distributed "id"
fileSuffix= strcat('Scan', num2str(selScan),'_Plate', num2str(1));
fileNamePlate = [filePrefix fileSuffix fileExt];
fileName= fullfile(resDir,'PrintResults', fileNamePlate); %[outputDirectory fileNamePlate];
%This,fprint for loop,is an very old legacy feature which slows processing. Could be
%removed but allows easy observation of how a run is progressing and can be
%used as a diagnostic tool.
outCprint= p4L4;
fid = fopen(fileName,'w');
fprintf(fid, 'Num.\tAUC\tMSR\tK\tr\tl\tR-squared\tK-lower\tK-upper\tr-lower\tr-upper\tl-upper\tl-lower\tArea\tLastInten\tSpineMaxRateTimePt\tLastFitTimePt\n');
for n=1:384 %startCount:numCultures
fprintf(fid,'%d\t',n);
fprintf(fid, '%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\n',...
outCprint{14,scanCnt}(n,1),outCprint{14,scanCnt}(n,2),outCprint{14,scanCnt}(n,3),outCprint{14,scanCnt}(n,4),...
outCprint{14,scanCnt}(n,5),outCprint{14,scanCnt}(n,6),outCprint{14,scanCnt}(n,7),outCprint{14,scanCnt}(n,8),...
outCprint{14,scanCnt}(n,9),outCprint{14,scanCnt}(n,10),outCprint{14,scanCnt}(n,11),outCprint{14,scanCnt}(n,12),...
outCprint{14,scanCnt}(n,13),outCprint{14,scanCnt}(n,14),outCprint{14,scanCnt}(n,15),outCprint{14,scanCnt}(n,16));
end
fclose(fid);
end
EASYconsole;
%+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

232
workflow/templates/qhtcp/ExpTemplate/Z_InteractionTemplate.R
View File

@@ -1,6 +1,15 @@
#Based on InteractionTemplate.R which is based on Sean Santose's Interaction_V5 script.
#Adapt SS For Structured Data storage but using command line scripts
###Set up the required libraries, call required plot theme elements and set up the command line arguments
#!/usr/bin/env R
# Based on InteractionTemplate.R which is based on Sean Santos's Interaction_V5 script
#
# Updated 2024 Bryan C Roessler to improve file operations and portability
# NOTE: The script now has 1 REQUIRED argument and 4 OPTIONAL arguments:
# 1. Path to input file
# 2. /output/ directory
# 3. Path to StudyInfo.csv
# 4. Path to SGDgeneList
# 5. Standard deviation value
# Load libraries
library("ggplot2")
library("plyr")
library("extrafont")
@@ -8,73 +17,76 @@ library("gridExtra")
library("gplots")
library("RColorBrewer")
library("stringr")
#library("gdata")
library(plotly)
library(htmlwidgets)
library("gdata")
library("plotly")
library("htmlwidgets")
Args <- commandArgs(TRUE)
input_file <- Args[1] #"!!Results_17_0827_yor1null-rpl12anull misLabeledAsFrom MI 17_0919_yor1-curated.txt" #Args[1] #Arg 1 #"!!ResultsStd_JS 19_1224_HLEG_P53.txt" is the !!results ... .txt
#Tool to find a file and copy it to desired location
destDir= getwd()
#srcFile= file.choose()
#file.copy(srcFile, destDir)
#input_file= tail(strsplit(srcFile,"[/]")[[1]],1)
# Parse arguments
args <- commandArgs(TRUE)
# Set input file (required)
inputFile <- args[1]
#Path to Output Directory
#W=getwd() #R is F'd up, Can't use, Any legitamate platform could build out dirs from this
outDir <- "ZScores/" #"Args[2] #paste0(W,"/ZScores/")
subDir <- outDir #Args[2]
if (file.exists(subDir)){
outputpath <- subDir
# Set output dir
if (length(args) > 2) {
outDir <- args[2]
} else {
dir.create(file.path(subDir))
outDir <- "/ZScores/"
}
if (file.exists(paste(subDir,"QC/",sep=""))){
outputpath_QC <- paste(subDir,"QC/",sep="")
# Set StudyInfo file path
if (length(args) > 3) {
studyInfo <- args[3]
} else {
dir.create(file.path(paste(subDir,"QC/",sep="")))
outputpath_QC <- paste(subDir,"QC/",sep="")
studyInfo <- "../Code/StudyInfo.csv"
}
#define the output path (formerly the second argument from Rscript)
outputpath <- outDir
#Set Args[2] the Background contamination noise filter as a function of standard deviation
#std= as.numeric(Args[2])
#Sean recommends 3 or 5 SD factor.
#Capture Exp_ number,use it to Save Args[2]{std}to Labels field and then Write to Labels to studyInfo.txt for future reference
Labels <- read.csv(file= "../Code/StudyInfo.csv",stringsAsFactors = FALSE) #,sep= ",")
print("Be sure to enter Background noise filter standard deviation i.e., 3 or 5 per Sean")
# Set SGDgeneList file path
if (length(args) > 4) {
SGDgeneList <- args[4]
} else {
SGDgeneList <- "../Code/SGD_features.tab"
}
# Set standard deviation
if (length(args) > 5) {
delBGFactor <- args[5]
} else {
# User prompt for std multiplier Value
cat("Enter a Standard Deviation value to noise filter \n")
inpChar<- readLines(file("stdin"), n = 1L)
cat(paste("Standard Deviation Value is", inpChar, "\n"))
inpNum= as.numeric(inpChar)
#set std deviation multiplier default if no user entry
if(!is.na(inpNum)){
std= inpNum
}else{std= 3}
print("Enter a Standard Deviation value for noise filter")
print("Sean Santos recommends 3 or 5")
delBGFactor <- readLines(file("stdin"), n = 1L)
}
delBGFactor <- as.numeric(delBGFactor)
if(is.na(delBGFactor)){
delBGFactor <- 3 # Recommended by Sean
}
print(paste("The Standard Deviation Value is: ", delBGFactor))
outDir_QC <- paste(outDir,"QC/",sep="")
if !(file.exists(outDir)){
dir.create(file.path(outDir))
}
if !(file.exists(outDir_QC)){
dir.create(file.path(outDir_QC))
}
# Capture Exp_ number,use it to Save args[2]{std}to Labels field and then
# write to Labels to studyInfo.txt for future reference
Labels <- read.csv(file=studyInfo,stringsAsFactors = FALSE) # sep= ","
expNumber <- as.numeric(sub("^.*?(\\d+)$", "\\1", getwd()))
Labels[expNumber,3]= as.numeric(std)
Delta_Background_sdFactor <- std
DelBGFactr <- as.numeric(Delta_Background_sdFactor)
#Write Background SD value to studyInfo.txt file
#write.csv(Labels,file=paste("../Code/StudyInfo.csv"),row.names = FALSE)
write.csv(Labels,file=paste("../Code/StudyInfo.csv"),row.names = FALSE)
print('ln 50 write StudyInfo.csv ')
#write.table(Labels,file=paste(outputpath,"StudyInfo.txt"),sep = "\t",row.names = FALSE)
Labels[expNumber,3] <- delBGFactor
write.csv(Labels,file=studyInfo,row.names = FALSE)
#++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
#++++++BEGIN USER DATA SELECTION SECTION+++++++++++++++++++++++++++++++++++++++++++++++++
###############################################################################
################### BEGIN USER DATA SELECTION SECTION #########################
###############################################################################
#read in the data
X <- read.delim(input_file,skip=2,as.is=T,row.names=1,strip.white=TRUE)
X <- read.delim(inputFile,skip=2,as.is=T,row.names=1,strip.white=TRUE)
X <- X[!(X[[1]]%in%c("","Scan")),]
#X <- X[!(X[[1]]%in%c(61:76)),] #Remove dAmp plates which are Scans 61 thru 76
@@ -145,7 +157,6 @@ Xbu= X
#Inserted to use SGDgenelist to update orfs and replace empty geneName cells with ORF name (adapted from Sean's Merge script). This is to 'fix' the naming for everything that follows (REMc, Heatmaps ... et.al) rather than do it piece meal later
#Sean's Match Script( which was adapted here) was fixed 2022_0608 so as not to write over the RF1&RF2 geneNames which caused a variance with his code results
#in the Z_lm_L,K,r&AUC output values. Values correlated well but were off by a multiplier factor.
SGDgeneList= "../Code/SGD_features.tab"
genes = data.frame(read.delim(file=SGDgeneList,quote="",header=FALSE,colClasses = c(rep("NULL",3), rep("character", 2), rep("NULL", 11))))
for(i in 1:length(X[,14])){
ii= as.numeric(i)
@@ -315,17 +326,17 @@ X$Delta_Backgrd <- X$LstBackgrd - X$X1stBackgrd
Raw_l_vs_K_beforeQC <- ggplot(X,aes(l,K,color=as.factor(Conc_Num))) + geom_point(aes(ORF=ORF,Gene=Gene,Delta_Backgrd=Delta_Backgrd),shape=3) +
ggtitle("Raw L vs K before QC") +
theme_Publication_legend_right()
pdf(paste(outputpath_QC,"Raw_L_vs_K_beforeQC.pdf",sep=""),width = 12,height = 8)
pdf(paste(outDir_QC,"Raw_L_vs_K_beforeQC.pdf",sep=""),width = 12,height = 8)
Raw_l_vs_K_beforeQC
dev.off()
pgg <- ggplotly(Raw_l_vs_K_beforeQC)
#pgg
plotly_path <- paste(getwd(),"/",outputpath_QC,"Raw_L_vs_K_beforeQC.html",sep="")
plotly_path <- paste(outDir_QC,"Raw_L_vs_K_beforeQC.html",sep="")
saveWidget(pgg, file=plotly_path, selfcontained =TRUE)
#set delta background tolerance based on 3 sds from the mean delta background
Delta_Background_Tolerance <- mean(X$Delta_Backgrd)+(DelBGFactr*sd(X$Delta_Backgrd))
Delta_Background_Tolerance <- mean(X$Delta_Backgrd)+(delBGFactor*sd(X$Delta_Backgrd))
#Delta_Background_Tolerance <- mean(X$Delta_Backgrd)+(3*sd(X$Delta_Backgrd))
print(paste("Delta_Background_Tolerance is",Delta_Background_Tolerance,sep=" "))
@@ -350,12 +361,12 @@ X_Delta_Backgrd_above_Tolerance_L_vs_K <- ggplot(X_Delta_Backgrd_above_Tolerance
annotate("text",x=X_Delta_Backgrd_above_Tolerance_L_halfmedian,y=X_Delta_Backgrd_above_Tolerance_K_halfmedian,
label = paste("Strains above delta background tolerance = ",X_Delta_Backgrd_above_Tolerance_toRemove)) +
theme_Publication_legend_right()
pdf(paste(outputpath_QC,"Raw_L_vs_K_for_strains_above_deltabackgrd_threshold.pdf",sep=""),width = 12,height = 8)
pdf(paste(outDir_QC,"Raw_L_vs_K_for_strains_above_deltabackgrd_threshold.pdf",sep=""),width = 12,height = 8)
X_Delta_Backgrd_above_Tolerance_L_vs_K
dev.off()
pgg <- ggplotly(X_Delta_Backgrd_above_Tolerance_L_vs_K)
#pgg
plotly_path <- paste(getwd(),"/",outputpath_QC,"Raw_L_vs_K_for_strains_above_deltabackgrd_threshold.html",sep="")
plotly_path <- paste(outDir_QC,"Raw_L_vs_K_for_strains_above_deltabackgrd_threshold.html",sep="")
saveWidget(pgg, file=plotly_path, selfcontained =TRUE)
#frequency plot for all data vs. the delta_background
@@ -366,7 +377,7 @@ DeltaBackground_Frequency_Plot <- ggplot(X,aes(Delta_Backgrd,color=as.factor(Con
DeltaBackground_Bar_Plot <- ggplot(X,aes(Delta_Backgrd,color=as.factor(Conc_Num))) + geom_bar() +
ggtitle("Bar plot for Delta Background by Conc All Data") + theme_Publication_legend_right()
pdf(file = paste(outputpath_QC,"Frequency_Delta_Background.pdf",sep=""),width = 12,height = 8)
pdf(file = paste(outDir_QC,"Frequency_Delta_Background.pdf",sep=""),width = 12,height = 8)
print(DeltaBackground_Frequency_Plot)
print(DeltaBackground_Bar_Plot)
dev.off()
@@ -432,7 +443,7 @@ Plate_Analysis_Delta_Backgrd_Box_afterQC <- ggplot(X,aes(as.factor(Scan),Delta_B
ggtitle("Plate analysis by Drug Conc for Delta_Backgrd after quality control") + theme_Publication()
#print the plate analysis data before and after QC
pdf(file=paste(outputpath_QC,"Plate_Analysis.pdf",sep=""),width = 14,height=9)
pdf(file=paste(outDir_QC,"Plate_Analysis.pdf",sep=""),width = 14,height=9)
Plate_Analysis_L
Plate_Analysis_L_afterQC
Plate_Analysis_K
@@ -446,7 +457,7 @@ Plate_Analysis_Delta_Backgrd_afterQC
dev.off()
#print the plate analysis data before and after QC
pdf(file=paste(outputpath_QC,"Plate_Analysis_Boxplots.pdf",sep=""),width = 18,height=9)
pdf(file=paste(outDir_QC,"Plate_Analysis_Boxplots.pdf",sep=""),width = 18,height=9)
Plate_Analysis_L_Box
Plate_Analysis_L_Box_afterQC
Plate_Analysis_K_Box
@@ -503,7 +514,7 @@ Plate_Analysis_Delta_Backgrd_Box_afterQC_Z <- ggplot(X_noZero,aes(as.factor(Scan
ggtitle("Plate analysis by Drug Conc for Delta_Backgrd after quality control") + theme_Publication()
#print the plate analysis data before and after QC
pdf(file=paste(outputpath_QC,"Plate_Analysis_noZeros.pdf",sep=""),width = 14,height=9)
pdf(file=paste(outDir_QC,"Plate_Analysis_noZeros.pdf",sep=""),width = 14,height=9)
Plate_Analysis_L_afterQC_Z
Plate_Analysis_K_afterQC_Z
Plate_Analysis_r_afterQC_Z
@@ -512,7 +523,7 @@ Plate_Analysis_Delta_Backgrd_afterQC_Z
dev.off()
#print the plate analysis data before and after QC
pdf(file=paste(outputpath_QC,"Plate_Analysis_noZeros_Boxplots.pdf",sep=""),width = 18,height=9)
pdf(file=paste(outDir_QC,"Plate_Analysis_noZeros_Boxplots.pdf",sep=""),width = 18,height=9)
Plate_Analysis_L_Box_afterQC_Z
Plate_Analysis_K_Box_afterQC_Z
Plate_Analysis_r_Box_afterQC_Z
@@ -556,7 +567,7 @@ X_stats_ALL <- ddply(X, c("Conc_Num","Conc_Num_Factor"), summarise,
)
#print(X_stats_ALL_L)
write.csv(X_stats_ALL,file=paste(outputpath,"SummaryStats_ALLSTRAINS.csv"),row.names = FALSE)
write.csv(X_stats_ALL,file=paste(outDir,"SummaryStats_ALLSTRAINS.csv"),row.names = FALSE)
#+++++END QC SECTION+++++++++++++++++++++++++++++++++++++++++++++++++++++++
##### Part 3 - Generate summary statistics and calculate the max theoretical L value
@@ -660,7 +671,7 @@ for(s in Background_Strains){
se_AUC = sd_AUC / sqrt(N-1)
)
write.csv(X_stats_BY,file=paste(outputpath,"SummaryStats_BackgroundStrains.csv"),row.names=FALSE)
write.csv(X_stats_BY,file=paste(outDir,"SummaryStats_BackgroundStrains.csv"),row.names=FALSE)
#calculate the max theoretical L values
#only look for max values when K is within 2SD of the ref strain
@@ -708,7 +719,7 @@ for(s in Background_Strains){
)
print(X_stats_BY_L_within_2SD_K)
X1_SD_within_2SD_K <- max(X_stats_BY_L_within_2SD_K$sd)
write.csv(X_stats_BY_L_within_2SD_K,file=paste(outputpath_QC,"Max_Observed_L_Vals_for_spots_within_2SD_K.csv",sep=""),row.names=FALSE)
write.csv(X_stats_BY_L_within_2SD_K,file=paste(outDir_QC,"Max_Observed_L_Vals_for_spots_within_2SD_K.csv",sep=""),row.names=FALSE)
X_stats_BY_L_outside_2SD_K <- ddply(X_outside_2SD_K, c("Conc_Num","Conc_Num_Factor"), summarise,
N = (length(l)),
@@ -725,22 +736,22 @@ for(s in Background_Strains){
#X1_SD_outside_2SD_K <- X[X$l %in% X1_SD_within_2SD_K$l,]
Outside_2SD_K_L_vs_K <- ggplot(X_outside_2SD_K,aes(l,K,color=as.factor(Conc_Num))) + geom_point(aes(ORF=ORF,Gene=Gene,Delta_Backgrd=Delta_Backgrd),shape=3) +
ggtitle("Raw L vs K for strains falling outside 2SD of the K mean at each conc") + theme_Publication_legend_right()
pdf(paste(outputpath_QC,"Raw_L_vs_K_for_strains_2SD_outside_mean_K.pdf",sep=""),width = 10,height = 8)
pdf(paste(outDir_QC,"Raw_L_vs_K_for_strains_2SD_outside_mean_K.pdf",sep=""),width = 10,height = 8)
print(Outside_2SD_K_L_vs_K)
dev.off()
pgg <- ggplotly(Outside_2SD_K_L_vs_K)
plotly_path <- paste(getwd(),"/",outputpath_QC,"RawL_vs_K_for_strains_outside_2SD_K.html",sep="")
plotly_path <- paste(outDir_QC,"RawL_vs_K_for_strains_outside_2SD_K.html",sep="")
saveWidget(pgg, file=plotly_path, selfcontained =TRUE)
Outside_2SD_K_delta_background_vs_K <- ggplot(X_outside_2SD_K,aes(Delta_Backgrd,K,color=as.factor(Conc_Num))) + geom_point(aes(l=l,ORF=ORF,Gene=Gene),shape=3,position="jitter") +
ggtitle("DeltaBackground vs K for strains falling outside 2SD of the K mean at each conc") + theme_Publication_legend_right()
pdf(paste(outputpath_QC,"DeltaBackground_vs_K_for_strains_2SD_outside_mean_K.pdf",sep=""),width = 10,height = 8)
pdf(paste(outDir_QC,"DeltaBackground_vs_K_for_strains_2SD_outside_mean_K.pdf",sep=""),width = 10,height = 8)
Outside_2SD_K_delta_background_vs_K
dev.off()
pgg <- ggplotly(Outside_2SD_K_delta_background_vs_K)
#pgg
plotly_path <- paste(getwd(),"/",outputpath_QC,"DeltaBackground_vs_K_for_strains_outside_2SD_K.html",sep="")
plotly_path <- paste(outDir_QC,"DeltaBackground_vs_K_for_strains_outside_2SD_K.html",sep="")
saveWidget(pgg, file=plotly_path, selfcontained =TRUE)
@@ -1160,7 +1171,7 @@ for(s in Background_Strains){
InteractionScores_RF <- InteractionScores_RF[order(InteractionScores_RF$Z_lm_L,decreasing=TRUE),]
InteractionScores_RF <- InteractionScores_RF[order(InteractionScores_RF$NG,decreasing=TRUE),]
write.csv(InteractionScores_RF,paste(outputpath,"RF_ZScores_Interaction.csv",sep=""),row.names=FALSE)
write.csv(InteractionScores_RF,paste(outDir,"RF_ZScores_Interaction.csv",sep=""),row.names=FALSE)
for(i in 1:num_genes_RF){
@@ -1234,7 +1245,7 @@ for(s in Background_Strains){
}
}
print("Pass RF ggplot loop")
write.csv(X_stats_interaction_ALL_RF_final,paste(outputpath,"RF_ZScore_Calculations.csv",sep=""),row.names = FALSE)
write.csv(X_stats_interaction_ALL_RF_final,paste(outDir,"RF_ZScore_Calculations.csv",sep=""),row.names = FALSE)
####### Part 5 - Get Zscores for Gene deletion strains
@@ -1564,7 +1575,7 @@ for(s in Background_Strains){
InteractionScores <- InteractionScores[order(InteractionScores$NG,decreasing=TRUE),]
df_order_by_OrfRep <- unique(InteractionScores$OrfRep)
#X_stats_interaction_ALL <- X_stats_interaction_ALL[order(X_stats_interaction_ALL$NG,decreasing=TRUE),]
write.csv(InteractionScores,paste(outputpath,"ZScores_Interaction.csv",sep=""),row.names=FALSE)
write.csv(InteractionScores,paste(outDir,"ZScores_Interaction.csv",sep=""),row.names=FALSE)
InteractionScores_deletion_enhancers_L <- InteractionScores[InteractionScores$Avg_Zscore_L >= 2,]
InteractionScores_deletion_enhancers_K <- InteractionScores[InteractionScores$Avg_Zscore_K <= -2,]
@@ -1588,16 +1599,16 @@ for(s in Background_Strains){
InteractionScores_deletion_enhancers_lm_Suppressors_AvgZscore_K <- InteractionScores_deletion_enhancers_lm_Suppressors_AvgZscore_K[!is.na(InteractionScores_deletion_enhancers_lm_Suppressors_AvgZscore_K$OrfRep),]
InteractionScores_deletion_enhancers_Avg_Zscore_Suppressors_lm_K <- InteractionScores_deletion_enhancers_Avg_Zscore_Suppressors_lm_K[!is.na(InteractionScores_deletion_enhancers_Avg_Zscore_Suppressors_lm_K$OrfRep),]
write.csv(InteractionScores_deletion_enhancers_L,paste(outputpath,"ZScores_Interaction_DeletionEnhancers_L.csv",sep=""),row.names=FALSE)
write.csv(InteractionScores_deletion_enhancers_K,paste(outputpath,"ZScores_Interaction_DeletionEnhancers_K.csv",sep=""),row.names=FALSE)
write.csv(InteractionScores_deletion_suppressors_L,paste(outputpath,"ZScores_Interaction_DeletionSuppressors_L.csv",sep=""),row.names=FALSE)
write.csv(InteractionScores_deletion_suppressors_K,paste(outputpath,"ZScores_Interaction_DeletionSuppressors_K.csv",sep=""),row.names=FALSE)
write.csv(InteractionScores_deletion_enhancers_and_Suppressors_L,paste(outputpath,"ZScores_Interaction_DeletionEnhancers_and_Suppressors_L.csv",sep=""),row.names=FALSE)
write.csv(InteractionScores_deletion_enhancers_and_Suppressors_K,paste(outputpath,"ZScores_Interaction_DeletionEnhancers_and_Suppressors_K.csv",sep=""),row.names=FALSE)
write.csv(InteractionScores_deletion_enhancers_lm_Suppressors_AvgZscore_L,paste(outputpath,"ZScores_Interaction_Suppressors_and_lm_Enhancers_L.csv",sep=""),row.names=FALSE)
write.csv(InteractionScores_deletion_enhancers_Avg_Zscore_Suppressors_lm_L,paste(outputpath,"ZScores_Interaction_Enhancers_and_lm_Suppressors_L.csv",sep=""),row.names=FALSE)
write.csv(InteractionScores_deletion_enhancers_lm_Suppressors_AvgZscore_K,paste(outputpath,"ZScores_Interaction_Suppressors_and_lm_Enhancers_K.csv",sep=""),row.names=FALSE)
write.csv(InteractionScores_deletion_enhancers_Avg_Zscore_Suppressors_lm_K,paste(outputpath,"ZScores_Interaction_Enhancers_and_lm_Suppressors_K.csv",sep=""),row.names=FALSE)
write.csv(InteractionScores_deletion_enhancers_L,paste(outDir,"ZScores_Interaction_DeletionEnhancers_L.csv",sep=""),row.names=FALSE)
write.csv(InteractionScores_deletion_enhancers_K,paste(outDir,"ZScores_Interaction_DeletionEnhancers_K.csv",sep=""),row.names=FALSE)
write.csv(InteractionScores_deletion_suppressors_L,paste(outDir,"ZScores_Interaction_DeletionSuppressors_L.csv",sep=""),row.names=FALSE)
write.csv(InteractionScores_deletion_suppressors_K,paste(outDir,"ZScores_Interaction_DeletionSuppressors_K.csv",sep=""),row.names=FALSE)
write.csv(InteractionScores_deletion_enhancers_and_Suppressors_L,paste(outDir,"ZScores_Interaction_DeletionEnhancers_and_Suppressors_L.csv",sep=""),row.names=FALSE)
write.csv(InteractionScores_deletion_enhancers_and_Suppressors_K,paste(outDir,"ZScores_Interaction_DeletionEnhancers_and_Suppressors_K.csv",sep=""),row.names=FALSE)
write.csv(InteractionScores_deletion_enhancers_lm_Suppressors_AvgZscore_L,paste(outDir,"ZScores_Interaction_Suppressors_and_lm_Enhancers_L.csv",sep=""),row.names=FALSE)
write.csv(InteractionScores_deletion_enhancers_Avg_Zscore_Suppressors_lm_L,paste(outDir,"ZScores_Interaction_Enhancers_and_lm_Suppressors_L.csv",sep=""),row.names=FALSE)
write.csv(InteractionScores_deletion_enhancers_lm_Suppressors_AvgZscore_K,paste(outDir,"ZScores_Interaction_Suppressors_and_lm_Enhancers_K.csv",sep=""),row.names=FALSE)
write.csv(InteractionScores_deletion_enhancers_Avg_Zscore_Suppressors_lm_K,paste(outDir,"ZScores_Interaction_Enhancers_and_lm_Suppressors_K.csv",sep=""),row.names=FALSE)
#get enhancers and suppressors for linear regression
InteractionScores_deletion_enhancers_L_lm <- InteractionScores[InteractionScores$Z_lm_L >= 2,]
@@ -1614,15 +1625,15 @@ for(s in Background_Strains){
InteractionScores_deletion_enhancers_and_Suppressors_L_lm <- InteractionScores_deletion_enhancers_and_Suppressors_L_lm[!is.na(InteractionScores_deletion_enhancers_and_Suppressors_L_lm$OrfRep),]
InteractionScores_deletion_enhancers_and_Suppressors_K_lm <- InteractionScores_deletion_enhancers_and_Suppressors_K_lm[!is.na(InteractionScores_deletion_enhancers_and_Suppressors_K_lm$OrfRep),]
write.csv(InteractionScores_deletion_enhancers_L_lm,paste(outputpath,"ZScores_Interaction_DeletionEnhancers_L_lm.csv",sep=""),row.names=FALSE)
write.csv(InteractionScores_deletion_enhancers_K_lm,paste(outputpath,"ZScores_Interaction_DeletionEnhancers_K_lm.csv",sep=""),row.names=FALSE)
write.csv(InteractionScores_deletion_suppressors_L_lm,paste(outputpath,"ZScores_Interaction_DeletionSuppressors_L_lm.csv",sep=""),row.names=FALSE)
write.csv(InteractionScores_deletion_suppressors_K_lm,paste(outputpath,"ZScores_Interaction_DeletionSuppressors_K_lm.csv",sep=""),row.names=FALSE)
write.csv(InteractionScores_deletion_enhancers_and_Suppressors_L_lm,paste(outputpath,"ZScores_Interaction_DeletionEnhancers_and_Suppressors_L_lm.csv",sep=""),row.names=FALSE)
write.csv(InteractionScores_deletion_enhancers_and_Suppressors_K_lm,paste(outputpath,"ZScores_Interaction_DeletionEnhancers_and_Suppressors_K_lm.csv",sep=""),row.names=FALSE)
write.csv(InteractionScores_deletion_enhancers_L_lm,paste(outDir,"ZScores_Interaction_DeletionEnhancers_L_lm.csv",sep=""),row.names=FALSE)
write.csv(InteractionScores_deletion_enhancers_K_lm,paste(outDir,"ZScores_Interaction_DeletionEnhancers_K_lm.csv",sep=""),row.names=FALSE)
write.csv(InteractionScores_deletion_suppressors_L_lm,paste(outDir,"ZScores_Interaction_DeletionSuppressors_L_lm.csv",sep=""),row.names=FALSE)
write.csv(InteractionScores_deletion_suppressors_K_lm,paste(outDir,"ZScores_Interaction_DeletionSuppressors_K_lm.csv",sep=""),row.names=FALSE)
write.csv(InteractionScores_deletion_enhancers_and_Suppressors_L_lm,paste(outDir,"ZScores_Interaction_DeletionEnhancers_and_Suppressors_L_lm.csv",sep=""),row.names=FALSE)
write.csv(InteractionScores_deletion_enhancers_and_Suppressors_K_lm,paste(outDir,"ZScores_Interaction_DeletionEnhancers_and_Suppressors_K_lm.csv",sep=""),row.names=FALSE)
write.csv(Labels,file=paste("../Code/StudyInfo.csv"),row.names = FALSE)
write.csv(Labels,file=paste(StudyInfo),row.names = FALSE)
print('ln 1570 write StudyInfo.csv after ')
#write.table(Labels,file=paste("../Code/StudyInfo.txt"),sep="\t",row.names = FALSE)
@@ -1697,7 +1708,7 @@ for(s in Background_Strains){
}
}
print("Pass Int ggplot loop")
write.csv(X_stats_interaction_ALL_final,paste(outputpath,"ZScore_Calculations.csv",sep=""),row.names = FALSE)
write.csv(X_stats_interaction_ALL_final,paste(outDir,"ZScore_Calculations.csv",sep=""),row.names = FALSE)
@@ -1706,7 +1717,7 @@ for(s in Background_Strains){
Blank <- ggplot(X2_RF) + geom_blank()
pdf(paste(outputpath,"InteractionPlots.pdf",sep=""),width = 16, height = 16, onefile = TRUE)
pdf(paste(outDir,"InteractionPlots.pdf",sep=""),width = 16, height = 16, onefile = TRUE)
X_stats_X2_RF <- ddply(X2_RF, c("Conc_Num","Conc_Num_Factor"), summarise,
mean_L = mean(l,na.rm=TRUE),
@@ -1863,7 +1874,7 @@ for(s in Background_Strains){
pdf(paste(outputpath,"RF_InteractionPlots.pdf",sep=""),width = 16, height = 16, onefile = TRUE)
pdf(paste(outDir,"RF_InteractionPlots.pdf",sep=""),width = 16, height = 16, onefile = TRUE)
X_stats_X2_RF <- ddply(X2_RF, c("Conc_Num","Conc_Num_Factor"), summarise,
mean_L = mean(l,na.rm=TRUE),
@@ -2155,7 +2166,7 @@ for(s in Background_Strains){
theme_Publication()
pdf(paste(outputpath,"RankPlots.pdf",sep=""),width = 18, height = 12, onefile = TRUE)
pdf(paste(outDir,"RankPlots.pdf",sep=""),width = 18, height = 12, onefile = TRUE)
grid.arrange(Rank_L_1SD,Rank_L_2SD,Rank_L_3SD,Rank_K_1SD,Rank_K_2SD,Rank_K_3SD,ncol=3,nrow=2)
grid.arrange(Rank_L_1SD_notext,Rank_L_2SD_notext,Rank_L_3SD_notext,Rank_K_1SD_notext,Rank_K_2SD_notext,Rank_K_3SD_notext,ncol=3,nrow=2)
@@ -2262,7 +2273,7 @@ for(s in Background_Strains){
geom_hline(yintercept=c(-3,3)) + geom_point(size=0.1,shape=3) +
theme_Publication()
pdf(paste(outputpath,"RankPlots_lm.pdf",sep=""),width = 18, height = 12, onefile = TRUE)
pdf(paste(outDir,"RankPlots_lm.pdf",sep=""),width = 18, height = 12, onefile = TRUE)
grid.arrange(Rank_L_1SD_lm,Rank_L_2SD_lm,Rank_L_3SD_lm,Rank_K_1SD_lm,Rank_K_2SD_lm,Rank_K_3SD_lm,ncol=3,nrow=2)
grid.arrange(Rank_L_1SD_notext_lm,Rank_L_2SD_notext_lm,Rank_L_3SD_notext_lm,Rank_K_1SD_notext_lm,Rank_K_2SD_notext_lm,Rank_K_3SD_notext_lm,ncol=3,nrow=2)
@@ -2297,7 +2308,7 @@ for(s in Background_Strains){
get_lm_AUC <- lm(X_NArm$Z_lm_AUC~X_NArm$Avg_Zscore_AUC)
AUC_lm <- summary(get_lm_AUC)
pdf(paste(outputpath,"Avg_Zscore_vs_lm_NA_rm.pdf",sep=""),width = 16, height = 12, onefile = TRUE)
pdf(paste(outDir,"Avg_Zscore_vs_lm_NA_rm.pdf",sep=""),width = 16, height = 12, onefile = TRUE)
print(ggplot(X_NArm,aes(Avg_Zscore_L,Z_lm_L)) + geom_point(aes(color=Overlap),shape=3) + geom_smooth(method = "lm",color=1) +
ggtitle("Avg Zscore vs lm L") +
@@ -2329,7 +2340,7 @@ for(s in Background_Strains){
pgg <- ggplotly(lm_v_Zscore_L)
#pgg
plotly_path <- paste(getwd(),"/",outputpath,"Avg_Zscore_vs_lm_NA_rm.html",sep="")
plotly_path <- paste(outDir,"Avg_Zscore_vs_lm_NA_rm.html",sep="")
saveWidget(pgg, file=plotly_path, selfcontained =TRUE)
X_NArm$L_Rank <- rank(X_NArm$Avg_Zscore_L)
@@ -2357,7 +2368,7 @@ for(s in Background_Strains){
num_genes_NArm2 <- (dim(X_NArm)[1])/2
pdf(paste(outputpath,"Avg_Zscore_vs_lm_ranked_NA_rm.pdf",sep=""),width = 16, height = 12, onefile = TRUE)
pdf(paste(outDir,"Avg_Zscore_vs_lm_ranked_NA_rm.pdf",sep=""),width = 16, height = 12, onefile = TRUE)
print(ggplot(X_NArm,aes(L_Rank,L_Rank_lm)) + geom_point(aes(color=Overlap),shape=3) + geom_smooth(method = "lm",color=1) +
ggtitle("Rank Avg Zscore vs lm L") +
@@ -2481,7 +2492,7 @@ for(s in Background_Strains){
theme_Publication()
pdf(paste(outputpath,"RankPlots_naRM.pdf",sep=""),width = 18, height = 12, onefile = TRUE)
pdf(paste(outDir,"RankPlots_naRM.pdf",sep=""),width = 18, height = 12, onefile = TRUE)
grid.arrange(Rank_L_1SD,Rank_L_2SD,Rank_L_3SD,Rank_K_1SD,Rank_K_2SD,Rank_K_3SD,ncol=3,nrow=2)
grid.arrange(Rank_L_1SD_notext,Rank_L_2SD_notext,Rank_L_3SD_notext,Rank_K_1SD_notext,Rank_K_2SD_notext,Rank_K_3SD_notext,ncol=3,nrow=2)
@@ -2588,7 +2599,7 @@ for(s in Background_Strains){
geom_hline(yintercept=c(-3,3)) + geom_point(size=0.1,shape=3) +
theme_Publication()
pdf(paste(outputpath,"RankPlots_lm_naRM.pdf",sep=""),width = 18, height = 12, onefile = TRUE)
pdf(paste(outDir,"RankPlots_lm_naRM.pdf",sep=""),width = 18, height = 12, onefile = TRUE)
grid.arrange(Rank_L_1SD_lm,Rank_L_2SD_lm,Rank_L_3SD_lm,Rank_K_1SD_lm,Rank_K_2SD_lm,Rank_K_3SD_lm,ncol=3,nrow=2)
grid.arrange(Rank_L_1SD_notext_lm,Rank_L_2SD_notext_lm,Rank_L_3SD_notext_lm,Rank_K_1SD_notext_lm,Rank_K_2SD_notext_lm,Rank_K_3SD_notext_lm,ncol=3,nrow=2)
@@ -2619,7 +2630,7 @@ get_lm_6 <- lm(X_NArm$Z_lm_AUC~X_NArm$Z_lm_r)
L_lm_6 <- summary(get_lm_6)
pdf(file=paste(outputpath,"Correlation_CPPs.pdf",sep=""),width = 10, height = 7, onefile = TRUE)
pdf(file=paste(outDir,"Correlation_CPPs.pdf",sep=""),width = 10, height = 7, onefile = TRUE)
ggplot(X_NArm,aes(Z_lm_L,Z_lm_K)) + geom_point(shape=3,color="gray70") +
geom_smooth(method="lm",color="tomato3") +
@@ -2707,24 +2718,7 @@ ggplot(X_NArm,aes(Z_lm_r,Z_lm_AUC)) + geom_point(shape=3,color="gray70") +
theme_Publication_legend_right() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), axis.text.x = element_text(size=16),axis.title.x = element_text(size=18), axis.text.y = element_text(size=16),axis.title.y = element_text(size=18))
dev.off()
#write.csv(Labels,file=paste("../Code/Parameters.csv"),row.names = FALSE)
timestamp()
#BoneYard***********************************************
#I'm thinking this parameter needs to be save somewhere "permanent' for the record so outputs can be reproduced.
#take this out of the Arguments. In Matlab I could for future in .mat file. Maybe I could save the SD Args[2] as part of the StudyInfo.txt.
#Corruptable but better than nothing.
#if(is.na(Args[2])){
# std=3
#}else {
# std= Arg[2]
#Delta_Background_sdFactor <- 2 #Args[3]
#DelBGFactr <- as.numeric(Delta_Background_sdFactor)
#}