Modularize joinInteractExps.R

workflow/.old/templates/qhtcp/Exp2/Z_InteractionTemplate.R

@@ -1,6 +1,6 @@
-#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
+# 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
 library("ggplot2")
 library("plyr")
 library("extrafont")
@@ -8,24 +8,13 @@ library("gridExtra")
 library("gplots")
 library("RColorBrewer")
 library("stringr")
-#library("gdata")
-library(plotly)
-library(htmlwidgets)
+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)
-
-
-
-#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]
+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
+outDir <- "ZScores/" #"args[2] #paste0(W,"/ZScores/")
+subDir <- outDir     #args[2]
 
 if (file.exists(subDir)){
   outputpath <- subDir
@@ -40,12 +29,12 @@ if (file.exists(paste(subDir,"QC/",sep=""))){
   outputpath_QC <- paste(subDir,"QC/",sep="")
 }
 #define the output path (formerly the second argument from Rscript)
-outputpath <- outDir 
+outputpath <- outDir
 
-#Set Args[2] the Background contamination noise filter as a function of standard deviation
-#std= as.numeric(Args[2])
+#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
+#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")
 
@@ -59,20 +48,17 @@ if(!is.na(inpNum)){
   std= inpNum
 }else{std= 3}
 
-
 expNumber<- as.numeric(sub("^.*?(\\d+)$", "\\1", getwd()))
 Labels[expNumber,3]= as.numeric(std)
 Delta_Background_sdFactor <- std
-DelBGFactr <- as.numeric(Delta_Background_sdFactor)
+delBGFactor <- 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)
 
-#++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-#++++++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 <- X[!(X[[1]]%in%c("","Scan")),]
@@ -325,7 +311,7 @@ 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=" "))
 
@@ -2718,13 +2704,13 @@ 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. 
+#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])){
+#if(is.na(args[2])){
 # std=3
 #}else {
 # std= Arg[2]
-#Delta_Background_sdFactor <- 2  #Args[3]
-#DelBGFactr <- as.numeric(Delta_Background_sdFactor)
+#Delta_Background_sdFactor <- 2  #args[3]
+#delBGFactor <- as.numeric(Delta_Background_sdFactor)
 #} 
 

workflow/.old/templates/qhtcp/Exp2/backups/InteractTemplateB4Prompt4SDinput.R

@@ -44,7 +44,7 @@ std= as.numeric(Args[2])
 expNumber<- as.numeric(sub("^.*?(\\d+)$", "\\1", getwd()))
 Labels[expNumber,3]= as.numeric(std)
 Delta_Background_sdFactor <- std
-DelBGFactr <- as.numeric(Delta_Background_sdFactor)
+delBGFactor <- 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)
@@ -297,7 +297,7 @@ 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=" "))
 
@@ -2697,6 +2697,6 @@ timestamp()
 #}else {
 # std= Arg[2]
 #Delta_Background_sdFactor <- 2  #Args[3]
-#DelBGFactr <- as.numeric(Delta_Background_sdFactor)
+#delBGFactor <- as.numeric(Delta_Background_sdFactor)
 #} 
 

workflow/.old/templates/qhtcp/Exp3/Z_InteractionTemplate.R

@@ -63,7 +63,7 @@ if(!is.na(inpNum)){
 expNumber<- as.numeric(sub("^.*?(\\d+)$", "\\1", getwd()))
 Labels[expNumber,3]= as.numeric(std)
 Delta_Background_sdFactor <- std
-DelBGFactr <- as.numeric(Delta_Background_sdFactor)
+delBGFactor <- 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)
@@ -325,7 +325,7 @@ 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=" "))
 
@@ -2725,6 +2725,6 @@ timestamp()
 #}else {
 # std= Arg[2]
 #Delta_Background_sdFactor <- 2  #Args[3]
-#DelBGFactr <- as.numeric(Delta_Background_sdFactor)
+#delBGFactor <- as.numeric(Delta_Background_sdFactor)
 #} 
 

workflow/.old/templates/qhtcp/Exp3/backups/InteractTemplateB4Prompt4SDinput.R

@@ -44,7 +44,7 @@ std= as.numeric(Args[2])
 expNumber<- as.numeric(sub("^.*?(\\d+)$", "\\1", getwd()))
 Labels[expNumber,3]= as.numeric(std)
 Delta_Background_sdFactor <- std
-DelBGFactr <- as.numeric(Delta_Background_sdFactor)
+delBGFactor <- 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)
@@ -297,7 +297,7 @@ 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=" "))
 
@@ -2697,6 +2697,6 @@ timestamp()
 #}else {
 # std= Arg[2]
 #Delta_Background_sdFactor <- 2  #Args[3]
-#DelBGFactr <- as.numeric(Delta_Background_sdFactor)
+#delBGFactor <- as.numeric(Delta_Background_sdFactor)
 #} 
 

workflow/.old/templates/qhtcp/Exp4/Z_InteractionTemplate.R

@@ -63,7 +63,7 @@ if(!is.na(inpNum)){
 expNumber<- as.numeric(sub("^.*?(\\d+)$", "\\1", getwd()))
 Labels[expNumber,3]= as.numeric(std)
 Delta_Background_sdFactor <- std
-DelBGFactr <- as.numeric(Delta_Background_sdFactor)
+delBGFactor <- 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)
@@ -325,7 +325,7 @@ 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=" "))
 
@@ -2725,6 +2725,6 @@ timestamp()
 #}else {
 # std= Arg[2]
 #Delta_Background_sdFactor <- 2  #Args[3]
-#DelBGFactr <- as.numeric(Delta_Background_sdFactor)
+#delBGFactor <- as.numeric(Delta_Background_sdFactor)
 #} 
 

workflow/.old/templates/qhtcp/Exp4/backups/InteractTemplateB4Prompt4SDinput.R

@@ -44,7 +44,7 @@ std= as.numeric(Args[2])
 expNumber<- as.numeric(sub("^.*?(\\d+)$", "\\1", getwd()))
 Labels[expNumber,3]= as.numeric(std)
 Delta_Background_sdFactor <- std
-DelBGFactr <- as.numeric(Delta_Background_sdFactor)
+delBGFactor <- 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)
@@ -297,7 +297,7 @@ 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=" "))
 
@@ -2697,6 +2697,6 @@ timestamp()
 #}else {
 # std= Arg[2]
 #Delta_Background_sdFactor <- 2  #Args[3]
-#DelBGFactr <- as.numeric(Delta_Background_sdFactor)
+#delBGFactor <- as.numeric(Delta_Background_sdFactor)
 #}