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hartman-server/workflow/apps/matlab/ezview/EZmultiGeneRFsLst.m

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%EZmultiGeneRFsLst Called by EZmultiExLoad
%Called by EZmultiExLoad about line173 Which is called by EZexpSel
%User Select Reference Gene and Specifics Added
%****Compile GeneList and OrfList,****************************************
%****Sort and add the medians of Ref Plates if RF1,RF2 exist**************
clear aa bb c uu vv drf drfPindx drfr drfc
clear RF1scanN RF2scanN
for mx=1:length(Exp(expN).Dexp(n).MP)
try
char((Exp(expN).Dexp(n).MP(mx).genename{1}(384)))
MPnum=mx;
catch
break
end
end
DMnum= length(Exp(expN).Dexp(n).DM.drug);
tPtsSize= size(Exp(expN).Dexp(n).FexpScanBMtp{1,1},(3)); %size(FexpScanBMtp{1,1},3);
%*********************************
lstindx=0;
lstindxOrf=0;
spN=0; Exp(expN).Dexp(n).RFrnames %<--???
rfcnt=0;
dRF1indx=0;
RF1mp=[]; RF2mp=[];
rfSp= cell2mat(rfSpec); %user entry of Specifics for Ref selection
%*******************************************************
for mp=1:MPnum
%RF1fullPlate=0;
for ind384=1:384
spN=spN+1;
try %
r= ceil(ind384/24);
if rem(ind384,24)==0, c=24; else c=rem(ind384,24); end
%Insert test for numeric in genename and orf if isnumeric
%Correct common EXCEL problem of converting OCT1 into a date numeric
if cell2mat(Exp(expN).Dexp(n).MP(mp).genename{1}(ind384))==38991,
Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)={'OCT1_'};
elseif isnumeric(cell2mat(Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)))
Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)={' '};
end
%****Check for full(384spot) Reference Plates (RF1 or/and RF2)**************
RF1fullPlate=0;
try RF1fullPlate=sum(ismember((Exp(expN).Dexp(n).MP(mp).genename{1}),rfGene))==384; catch, mp, msg=strcat(num2str(mp),' genename ERROR'), end
RF2fullPlate=0;
try RF2fullPlate=sum(ismember((Exp(expN).Dexp(n).MP(mp).genename{1}),'RF2'))==384; catch, mp, msg=strcat(num2str(mp),' genename ERROR'), end
%*************************************************************************
%Capture non-reference spot location and ORF data
if isempty(regexpi(char((Exp(expN).Dexp(n).MP(mp).orf{1}(ind384))),'blank'))... %'\<blank\>'
&& ~isnumeric(Exp(expN).Dexp(n).MP(mp).orf{1}(ind384))...
&& ~strcmpi((Exp(expN).Dexp(n).MP(mp).orf{1}(ind384)),' ')...
&& ~strcmpi((Exp(expN).Dexp(n).MP(mp).orf{1}(ind384)),' ')...
&& ~strcmpi((Exp(expN).Dexp(n).MP(mp).orf{1}(ind384)),'')...
&& ~isempty((Exp(expN).Dexp(n).MP(mp).orf{1}(ind384)))...
&& ((~strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),rfGene)|| ~strcmpi((Exp(expN).Dexp(n).MP(mp).specifics{1}(ind384)),rfSp))&&...
(~strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),rfGene)|| ~strcmpi(rfSp,'None')))...
&& ((~strcmpi((Exp(expN).Dexp(n).MP(mp).orf{1}(ind384)),rfGene)|| ~strcmpi((Exp(expN).Dexp(n).MP(mp).specifics{1}(ind384)),rfSp))&&...
(~strcmpi((Exp(expN).Dexp(n).MP(mp).orf{1}(ind384)),rfGene)|| ~strcmpi(rfSp,'None')))...
&& (~strcmpi((Exp(expN).Dexp(n).MP(mp).orf{1}(ind384)),'RF2')||~strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),'RF2'))...
&& iscellstr((Exp(expN).Dexp(n).MP(mp).orf{1}(ind384)))
lstindxOrf=lstindxOrf+1;
Exp(expN).Dexp(n).MP(mp).orf{1}(ind384) =strrep((Exp(expN).Dexp(n).MP(mp).orf{1}(ind384)),':',' ');
bb(lstindxOrf,1)= (Exp(expN).Dexp(n).MP(mp).orf{1}(ind384));
bb(lstindxOrf,2)={strcat(':',num2str(mp),':',num2str(r),':',num2str(c))};
bb(lstindxOrf,3)={mp};
bb(lstindxOrf,4)={r};
bb(lstindxOrf,5)={c};
mutorfs(lstindxOrf)=spN; %16_0318 added for Interaction EZinteract
%Exp(expN).Dexp(n).mutSpotIndx(lstindxOrf)=spN; %16_0318 added for Interaction EZinteract
end
%Capture non-reference spot location and GENENAME data
if isempty(regexpi(char((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384))),'blank'))... %'\<blank\>'
&& ~isnumeric(Exp(expN).Dexp(n).MP(mp).genename{1}(ind384))...
&& ~strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),' ')...
&& ~strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),' ')...
&& ~strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),'')...
&& ~isempty((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)))...
&& (~strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),rfGene) || ~strcmpi((Exp(expN).Dexp(n).MP(mp).specifics{1}(ind384)),rfSp))&&... % AddSpecifics rfSp && ~RF1fullPlate)...
(~strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),rfGene) || ~strcmpi(rfSp,'None'))...
&& (~strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),'RF2'))... %&& ~RF2fullPlate)...
&& iscellstr((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)))
lstindx=lstindx+1;
Exp(expN).Dexp(n).MP(mp).genename{1}(ind384) =strrep((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),':',' ');
aa(lstindx,1)= (Exp(expN).Dexp(n).MP(mp).genename{1}(ind384));
aa(lstindx,2)= {strcat(':',num2str(mp),':',num2str(r),':',num2str(c))};
aa(lstindx,3)={mp};
aa(lstindx,4)={r};
aa(lstindx,5)={c};
mutgenes(lstindx)=spN;
elseif (RF1fullPlate==1 ||... %sum(ismember((Exp(expN).Dexp(n).MP(mp).genename{1}),rfGene))==384 || ...
(((length(unique(Exp(expN).Dexp(n).MP(mp).genename{1}(1:384)))) ==1 && mp==1 ) && ... %(isequal((Exp(expN).Dexp(n).MP(mp).genename{1}(1:384)), (Exp(expN).Dexp(n).MP(mp).genename{1}(384:-1:1)))&& mp==1 )) && ...
~exist('RF1scanN','var')))
RF1mp=mp
RF1scanN=(mp*DMnum)-(DMnum-1) %mp;
rfcnt=rfcnt+1;
RFs(spN:spN+383)= spN:spN+383;
elseif (RF2fullPlate==1|| ... %sum(ismember((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),'RF2'))==384 ||...
(((length(unique(Exp(expN).Dexp(n).MP(mp).genename{1}(1:384)))) ==1 && mp== MPnum ) && ...
~exist('RF2scanN','var')))
RF2mp=mp
rfcnt=rfcnt+1;
RFs(spN:spN+383)= spN:spN+383;
RF2scanN= (mp*DMnum)-(DMnum-1) %mp;
%DISPersed REFerence capture and find Medians
elseif ( ((strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),rfGene) && ...
strcmpi((Exp(expN).Dexp(n).MP(mp).specifics{1}(ind384)),rfSp)))...
|| ((strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),rfGene) && ...
strcmpi(rfSp,'None'))) )...
&& (RF1fullPlate~=1),
dRF1indx=dRF1indx+1;
Exp(expN).Dexp(n).MP(mp).genename{1}(ind384) =strrep((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),':',' ');
drf(dRF1indx,1)= (Exp(expN).Dexp(n).MP(mp).genename{1}(ind384));
drf(dRF1indx,2)= {strcat(':',num2str(mp),':',num2str(r),':',num2str(c))};
drf(dRF1indx,3)={mp}; drfMP(dRF1indx,mp)= mp;
drf(dRF1indx,4)={r}; drfr(dRF1indx,mp)= r;
drf(dRF1indx,5)={c}; drfc(dRF1indx,mp)= c;
drf(dRF1indx,6)={ind384}; drfPindx(dRF1indx,mp)= ind384;
%drf(dRF1indx,7)= (Exp(expN).Dexp(n).MP(mp).specifics{1}(ind384));
end %if isempty(regexpi(char((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384))),'blank'))...
%*******************************************************************************
catch
error='EZexpSel lineAfter 24 EZmultiGeneLst.m'
mp %Disable in future to prevent a bomb out OR put into a nested TryCatch
ind384 %Disable in future to prevent a bomb out OR put into a nested TryCatch
msgBadGeneName= strcat('check genename at mp=',num2str(mp),' indx=',num2str(ind384))
end
end %end associated with for ind384=1:384
mp
end %end associated with for mp=1:length(Exp(expN).Dexp(n).MP)
%*****************************************************
%Cover case if mutorfs RFs are labeled RF1 or RF2
try
Exp(expN).Dexp(n).mutSpotIndx.wRFs= union(RFs, mutorfs);
catch
msg= 'No RFs Found in Exp! wRFs'
Exp(expN).Dexp(n).mutSpotIndx.wRFs= mutorfs;
end
try
Exp(expN).Dexp(n).mutSpotIndx.woRFs= setdiff(mutorfs,RFs);
catch
msg= 'No RFs Found in Exp! woRFs'
Exp(expN).Dexp(n).mutSpotIndx.woRFs= mutorfs;
end
%&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&
Exp(expN).Dexp(n).RFmd1indx=[];
Exp(expN).Dexp(n).RFmd1pltN=[];
Exp(expN).Dexp(n).RFmd1LB= {[]};
Exp(expN).Dexp(n).RFmd1indx= [];
Exp(expN).Dexp(n).RFmd1pltN={};
Exp(expN).Dexp(n).RFmd1val= [];
Exp(expN).Dexp(n).mean1= [];
Exp(expN).Dexp(n).std1= [];
Exp(expN).Dexp(n).min1= [];
Exp(expN).Dexp(n).max1= [];
Exp(expN).Dexp(n).RFcmpK= []; %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpr= []; %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpL= []; %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFmd2LB= {[]};
Exp(expN).Dexp(n).RFmd2indx= [];
Exp(expN).Dexp(n).RFmd2pltN= [];
Exp(expN).Dexp(n).RFmd2val= [];
Exp(expN).Dexp(n).mean2= [];
Exp(expN).Dexp(n).std2= [];
Exp(expN).Dexp(n).min2= [];
Exp(expN).Dexp(n).max2= [];
Exp(expN).Dexp(n).RFmean= [];
Exp(expN).Dexp(n).RFstd= [];
Exp(expN).Dexp(n).RFmin= [];
Exp(expN).Dexp(n).RFmax= [];
Exp(expN).Dexp(n).RFmdPLB= {[]};
Exp(expN).Dexp(n).RFmdPindx= [];
Exp(expN).Dexp(n).RFmdPpltN= [];
Exp(expN).Dexp(n).RFmdPscanN= [];
Exp(expN).Dexp(n).RFmedianP= [];
Exp(expN).Dexp(n).stdP= [];
Exp(expN).Dexp(n).meanP= [];
Exp(expN).Dexp(n).minP= [];
Exp(expN).Dexp(n).maxP= [];
Exp(expN).Dexp(n).RFmdGLB= {[]};
Exp(expN).Dexp(n).RFmdGindx= [];
Exp(expN).Dexp(n).RFmdGpltN= [];
Exp(expN).Dexp(n).RFmdGscanN= [];
Exp(expN).Dexp(n).RFmedianG= [];
Exp(expN).Dexp(n).RFminG= [];
Exp(expN).Dexp(n).RFmaxG= [];
Exp(expN).Dexp(n).RFstdG= [];
Exp(expN).Dexp(n).RFmeanG= [];
Exp(expN).Dexp(n).RFcmpGK= []; %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpGr= []; %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpGL= []; %For Ref Composite 17_1009
if exist('RF1scanN','var')
for d=0:(DMnum-1)
medianIndx=[];
nonZeroIndx=[];
medValList=[];
rf1scN=RF1scanN+d;
try %if RF1scanN doesn't exist this addition to list will be skipped
nonZeroIndx= find(Exp(expN).Dexp(n).scan(rf1scN).plate(1).CFout(1:384,5));
if isempty(nonZeroIndx), nonZeroCnt=0, medianIndx= nonZeroIndx;
else nonZeroCnt=length(nonZeroIndx);
end
%
if ~isempty(nonZeroIndx) && mod(nonZeroCnt,2)==0, medianIndx= nonZeroIndx(1:nonZeroCnt-1); end
if ~isempty(nonZeroIndx) && mod(nonZeroCnt,2)~=0, medianIndx= nonZeroIndx; end
clear medValLst
clear kValLst
clear rValLst
if ~isempty(nonZeroIndx) && length(medianIndx) > (.15*384) %To calc. a median, more than 15% of spots must be nonZero
medValLst= Exp(expN).Dexp(n).scan(rf1scN).plate(1).CFout(medianIndx,5);
medValList1{d+1}= medValLst;
min1= min(medValLst);
max1= max(medValLst);
std1= std(medValLst);
mean1= mean(medValLst);
kValLst= Exp(expN).Dexp(n).scan(rf1scN).plate(1).CFout(medianIndx,3); %For Ref Composite 17_1009
rValLst= Exp(expN).Dexp(n).scan(rf1scN).plate(1).CFout(medianIndx,4); %For Ref Composite 17_1009
mval1=median(medValLst); %mval1=median(Exp(expN).Dexp(n).scan(RF1mps).plate(1).CFout(1:384,5)); %CFout(1:383,5));
RFmd1pos=find(mval1==(Exp(expN).Dexp(n).scan(rf1scN).plate(1).CFout(1:384,5)));
RFmd1loc(1)= ceil(RFmd1pos/24); %calc r value
RFmd1loc(2)= RFmd1pos - ((RFmd1loc(1)-1)*24); %calc c value
lstindx=lstindx+1;
lstindxOrf= lstindxOrf+1;
aa(lstindx,1)= {strcat('RF1md(',num2str(d+1),')')}; %{'RF1md'};
aa(lstindx,2)= {strcat(':',num2str(RF1mp),':',num2str(RFmd1loc(1)),':',num2str(RFmd1loc(2)))}; %,'std_',num2str(std1))};
bb(lstindxOrf,1)= {strcat('RF1md(',num2str(d+1),')')}; %remove string2cell brackets {...} %{'RF1md'};
bb(lstindxOrf,2)={strcat(':',num2str(RF1mp),':',num2str(RFmd1loc(1)),':',num2str(RFmd1loc(2)))}; %,'std_',num2str(std1))};
%Composite Reference Amalgum Plot **********************
lstindx=lstindx+1;
lstindxOrf= lstindxOrf+1;
aa(lstindx,1)= {strcat('RF1cmp(',num2str(d+1),')')};
aa(lstindx,2)={''};
bb(lstindxOrf,1)= {strcat('RF1cmp(',num2str(d+1),')')};
bb(lstindxOrf,2)={''};
%********************************************************
Exp(expN).Dexp(n).RFmd1LB(d+1)= strcat(aa(lstindx,1),aa(lstindx,2));
Exp(expN).Dexp(n).RFmd1indx(d+1)= RFmd1pos;
Exp(expN).Dexp(n).RFmd1pltN= RF1mp;
Exp(expN).Dexp(n).RFmd1val(d+1)= mval1;
Exp(expN).Dexp(n).mean1(d+1)= mean1;
Exp(expN).Dexp(n).std1(d+1)= std1;
Exp(expN).Dexp(n).min1(d+1)= min1;
Exp(expN).Dexp(n).max1(d+1)= max1;
Exp(expN).Dexp(n).RFcmpL(1).dm(d+1).Lvals= medValLst; %17_1201 TrendOL
Exp(expN).Dexp(n).RFcmpL(1).dm(d+1).med= median(medValLst); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpL(1).dm(d+1).mean= mean(medValLst); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpL(1).dm(d+1).std= std(medValLst); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpL(1).dm(d+1).min= min(medValLst); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpL(1).dm(d+1).max= max(medValLst); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpK(1).dm(d+1).Kvals= kValLst;
Exp(expN).Dexp(n).RFcmpK(1).dm(d+1).med= median(kValLst); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpK(1).dm(d+1).mean= mean(kValLst); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpK(1).dm(d+1).std= std(kValLst); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpK(1).dm(d+1).min= min(kValLst); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpK(1).dm(d+1).max= max(kValLst); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpr(1).dm(d+1).rvals= rValLst;
Exp(expN).Dexp(n).RFcmpr(1).dm(d+1).med= median(rValLst); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpr(1).dm(d+1).mean= mean(rValLst); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpr(1).dm(d+1).std= std(rValLst); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpr(1).dm(d+1).min= min(rValLst); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpr(1).dm(d+1).max= max(rValLst); %For Ref Composite 17_1009
else
% Need to set L r K values to zeros or pick the first spot with zeros
%Spot 1 could be other than zero as the median isn't calculated if
%fewer than some percent are nonzero
medianCalcFailed= 'To Few nonZero spots for valid median RF1 selection'
firstZero= find(((Exp(expN).Dexp(n).scan(rf1scN).plate(1).CFout(1:384,5))==0),1,'first')
Exp(expN).Dexp(n).RFmd1indx(d+1)=firstZero;
Exp(expN).Dexp(n).RFmd1pltN= RF1mp;
try medValList1{d+1}= Exp(expN).Dexp(n).scan(rf1scN).plate(1).CFout(medianIndx,5); nonZeroCnt; catch, catcherror='Ln356', end
end %~isempty(nonZeroIndx) && length(medianIndx) > (.15*384)
catch %try ~ln375
medianCalcTryFailed1= 'Failed! Failed! Ln362 But process continued with placeholder P1ind384 spot value!'
try
firstZero= find(((Exp(expN).Dexp(n).scan(rf1scN).plate(1).CFout(1:384,5))==0),1,'first')
Exp(expN).Dexp(n).RFmd1indx(d+1)=firstZero;
catch
catchissue='Ln209'
Exp(expN).Dexp(n).RFmd1indx(d+1)=384; %if crapout,Then use spot384 as default to keep going
end
try
Exp(expN).Dexp(n).RFmd1pltN= RF1mp;
catch
catchissue='Ln209'
Exp(expN).Dexp(n).RFmd1pltN= 1;
end
error='EZexpSel lineAfter 209'
end %try ~ln209
end %for d=0:DMnum
end % if exist('RF1scanN','var')
%**********************************************************************************
%Calc RF2 median if a full plate of RF2s exist**************************
Exp(expN).Dexp(n).RFmd2indx=[];
Exp(expN).Dexp(n).RFmd2pltN=[];
if exist('RF2scanN','var')
for d=0:(DMnum-1)
medianIndx2=[];
nonZeroIndx2=[];
medValList2=[];
rf2scN=RF2scanN+d;
try %if RF2scanN doesn't exist this addition to list will be skipped
nonZeroIndx2= find(Exp(expN).Dexp(n).scan(rf2scN).plate(1).CFout(1:384,5));
if isempty(nonZeroIndx2), nonZeroCnt2=0; medianIndx2= nonZeroIndx2;
else nonZeroCnt2=length(nonZeroIndx2);
end
%
if ~isempty(nonZeroIndx2) && mod(nonZeroCnt2,2)==0, medianIndx2= nonZeroIndx2(1:nonZeroCnt2-1); end
if ~isempty(nonZeroIndx2) && mod(nonZeroCnt2,2)~=0, medianIndx2= nonZeroIndx2; end
clear medValLst2
clear kValLst2
clear rValLst2
if ~isempty(nonZeroIndx2) && length(medianIndx2) > (.15*384) %To calc. a median, more than 15% of spots must be nonZero
medValLst2= Exp(expN).Dexp(n).scan(rf2scN).plate(1).CFout(medianIndx2,5);
medValList2{d+1}= medValLst2;
min2= min(medValLst2);
max2= max(medValLst2);
std2= std(medValLst2);
mean2= mean(medValLst2);
kValLst2= Exp(expN).Dexp(n).scan(rf2scN).plate(1).CFout(medianIndx2,3); %For Ref Composite 17_1009
rValLst2= Exp(expN).Dexp(n).scan(rf2scN).plate(1).CFout(medianIndx2,4); %For Ref Composite 17_1009
mval2=median(medValLst2); %mval2=median(Exp(expN).Dexp(n).scan(RF2mps).plate(1).CFout(1:383,5));
RFmd2pos=find(mval2==(Exp(expN).Dexp(n).scan(rf2scN).plate(1).CFout(1:384,5)));
RFmd2loc(1)= ceil(RFmd2pos/24); %calc r value
RFmd2loc(2)= RFmd2pos - ((RFmd2loc(1)-1)*24); %calc c value
lstindx=lstindx+1;
lstindxOrf= lstindxOrf+1;
aa(lstindx,1)= {strcat('RF2md(',num2str(d+1),')')}; %{'RF2md'};
aa(lstindx,2)= {strcat(':',num2str(RF2mp),':',num2str(RFmd2loc(1)),':',num2str(RFmd2loc(2)))}; %,'std_',num2str(std2))};
bb(lstindxOrf,1)= {strcat('RF2md(',num2str(d+1),')')}; %remove string2cell brackets {...} %{'RF2md'};
bb(lstindxOrf,2)={strcat(':',num2str(RF2mp),':',num2str(RFmd2loc(1)),':',num2str(RFmd2loc(2)))}; %,'std_',num2str(std2))};
%Composite Reference Amalgum Plot (CRAP)
lstindx=lstindx+1;
lstindxOrf= lstindxOrf+1;
aa(lstindx,1)= {strcat('RF2cmp(',num2str(d+1),')')};
aa(lstindx,2)={''};
bb(lstindxOrf,1)= {strcat('RF2cmp(',num2str(d+1),')')};
bb(lstindxOrf,2)={''};
Exp(expN).Dexp(n).RFmd2LB(d+1)= strcat(aa(lstindx,1),aa(lstindx,2));
Exp(expN).Dexp(n).RFmd2indx(d+1)=RFmd2pos;
Exp(expN).Dexp(n).RFmd2pltN= RF2mp;
Exp(expN).Dexp(n).RFmd2val(d+1)= mval2;
Exp(expN).Dexp(n).mean2(d+1)= mean2;
Exp(expN).Dexp(n).std2(d+1)= std2;
Exp(expN).Dexp(n).min2(d+1)= min2;
Exp(expN).Dexp(n).max2(d+1)= max2;
Exp(expN).Dexp(n).RFcmpL(2).dm(d+1).Lvals= medValLst2; %17_1201 TrendOL
Exp(expN).Dexp(n).RFcmpL(2).dm(d+1).med= median(medValLst2); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpL(2).dm(d+1).mean= mean(medValLst2); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpL(2).dm(d+1).std= std(medValLst2); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpL(2).dm(d+1).min= min(medValLst2); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpL(2).dm(d+1).max= max(medValLst2); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpK(2).dm(d+1).Kvals= kValLst2;
Exp(expN).Dexp(n).RFcmpK(2).dm(d+1).med= median(kValLst2); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpK(2).dm(d+1).mean= mean(kValLst2); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpK(2).dm(d+1).std= std(kValLst2); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpK(2).dm(d+1).min= min(kValLst2); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpK(2).dm(d+1).max= max(kValLst2); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpr(2).dm(d+1).rvals= rValLst2;
Exp(expN).Dexp(n).RFcmpr(2).dm(d+1).med= median(rValLst2); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpr(2).dm(d+1).mean= mean(rValLst2); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpr(2).dm(d+1).std= std(rValLst2); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpr(2).dm(d+1).min= min(rValLst2); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpr(2).dm(d+1).max= max(rValLst); %For Ref Composite 17_1009
else
% Pick the first spot with zeros
% Use that position to satisfy and keep process OK
medianCalcFailed2= 'To Few nonZero spots for valid median RF2 selection'
firstZero2= find(((Exp(expN).Dexp(n).scan(rf2scN).plate(1).CFout(1:384,5))==0),1,'first')
Exp(expN).Dexp(n).RFmd2indx(d+1)=firstZero2;
Exp(expN).Dexp(n).RFmd2pltN= RF2mp;
try medValList2{d+1}= Exp(expN).Dexp(n).scan(rf2scN).plate(1).CFout(medianIndx2,5); nonZeroCnt2; catch, catchissue='Ln431', end
end
catch
medianCalcTryFailed2= 'Failed! Failed! Ln436 No RF1median But process continued with placeholder P1ind384 spot value!'
try
firstZero2= find(((Exp(expN).Dexp(n).scan(rf2scN).plate(1).CFout(1:384,5))==0),1,'first');
Exp(expN).Dexp(n).RFmd2indx(d+1)=firstZero2;
catch
catchissue='Ln442'
Exp(expN).Dexp(n).RFmd2indx(d+1)=384; %if crapout,Then use spot384 as default to keep going
end
try
Exp(expN).Dexp(n).RFmd2pltN= RF2mp;
catch
catchissue='Ln448'
Exp(expN).Dexp(n).RFmd2pltN= 1;
end
error='EZexpSel lineAfter 279'
end %if RF2scanN doesn't exist this addition to list will be skipped
clear RFcombValList
RFcombValList= cat(1,medValList1{d+1},medValList2{d+1});
Exp(expN).Dexp(n).RFmean(d+1)= mean(RFcombValList);
Exp(expN).Dexp(n).RFstd(d+1)=std(RFcombValList);
try, Exp(expN).Dexp(n).RFmin(d+1)= min(RFcombValList);
catch, Exp(expN).Dexp(n).RFmin(d+1)= 0; end
try, Exp(expN).Dexp(n).RFmax(d+1)=max(RFcombValList);
catch, Exp(expN).Dexp(n).RFmax(d+1)= 0; end
end %for d=0:DMnum ln446
elseif exist('RF1scanN','var')
Exp(expN).Dexp(n).RFmean= Exp(expN).Dexp(n).mean1;
Exp(expN).Dexp(n).RFstd= Exp(expN).Dexp(n).std1;
Exp(expN).Dexp(n).RFmin= Exp(expN).Dexp(n).min1;
Exp(expN).Dexp(n).RFmax= Exp(expN).Dexp(n).max1;
end %if exist('RF2scanN','var') ln445
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%*************************************************************************************************
%***********DISPERSE REFERENCE PLATES
Exp(expN).Dexp(n).RFmdPindx=[];
Exp(expN).Dexp(n).RFmdPpltN=[];
if exist('drf','var') %('RF1scanN','var')
%Det. index of change from one MP to the next
i=2;
clear chgIndx
chgIndx(1)=1;
for j=1:length(drf(:,3))
if j>1
if cell2mat(drf(j,3))~= cell2mat(drf((j-1),3)), chgIndx(i)=j; i=i+1; end
end
end
chgIndx(length(chgIndx)+1)= length(drf)+1;
uu=zeros(size(drf,1),4);
uu(:,1:4)= cell2mat(drf(:,3:6));
vv= zeros(size(drf,1),DMnum); %(length(drf),DMnum);
%************************************
dMPs= unique(cell2mat(drf(:,3)));
%*****************************************
%{
for mm=1:MPnum
nonZrfIndx.mp{mm,:}=drfPindx((find(drfPindx(:,mm))),mm);
end
%}
%nzValsG= zeros(DMnum,size(drf,1));
%nzValsAcc= zeros(DMnum,384);
for mm=1:length(dMPs) % length(chgIndx)
for d=1:(DMnum)
medianIndxDisp=[];
NZrefIndxP=[];
nonZeroValsP=[];
medValLstDisp=[];
rf1scNdisp=((dMPs(mm)-1)*DMnum)+(d);
try % Determine the dispersed RFs median mean and std if such exist
NZrefIndxP= drfPindx((find(drfPindx(:,dMPs(mm)))),dMPs(mm)); %find(Exp(expN).Dexp(n).scan(rf1scNdisp).plate(1).CFout(drf(chgIndx(cI):chgIndx(cI+1)),5));
%vv= Exp(expN).Dexp(n).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5);
vv(chgIndx(mm):(chgIndx(mm+1)-1),d)=Exp(expN).Dexp(n).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5);
%For Global Ref Composite 17_1009 %**************************************************************************
vvK(chgIndx(mm):(chgIndx(mm+1)-1),d)=Exp(expN).Dexp(n).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,3);
vvr(chgIndx(mm):(chgIndx(mm+1)-1),d)=Exp(expN).Dexp(n).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,4);
%*****************************************************************************************************
nonZeroValsP= nonzeros(Exp(expN).Dexp(n).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5));
std1Disp= std(nonZeroValsP);
mean1Disp= mean(nonZeroValsP);
minDisp= min(nonZeroValsP);
maxDisp= max(nonZeroValsP);
drfVals=Exp(expN).Dexp(n).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5);
%nzValsAcc(mm).DM(d,:)= nonZeroValsP;
%MEDIAN Determination for PLATES with Dispersed RFs
%NZrefIndxP= NZrefIndxP %find(Exp(expN).Dexp(n).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5));
if isempty(NZrefIndxP), nonZeroCntDisp=0, medianIndxDisp= NZrefIndxP;
else nonZeroCntDisp=length(NZrefIndxP);
end
if ~isempty(NZrefIndxP) && mod(nonZeroCntDisp,2)==0, medianIndxDisp= NZrefIndxP(1:nonZeroCntDisp-1); end
if ~isempty(NZrefIndxP) && mod(nonZeroCntDisp,2)~=0, medianIndxDisp= NZrefIndxP; end
if ~isempty(NZrefIndxP) && length(medianIndxDisp) > 0 %(.15*384) %To calc. a median, more than 15% of spots must be nonZero
medValLstDisp= Exp(expN).Dexp(n).scan(rf1scNdisp).plate(1).CFout(medianIndxDisp,5);
%medValList1Disp{d}= medValLstDisp;
mval1Disp=median(medValLstDisp); %mval1=median(Exp(expN).Dexp(n).scan(RF1mps).plate(1).CFout(1:384,5)); %CFout(1:383,5));
nonZeroMedPosIndx=find(mval1Disp==nonZeroValsP); %(Exp(expN).Dexp(n).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5))); %(nonZeroIndxDisp,5))); %((nonZrfIndx.mp{dMPs(mm),:}),5)));
RFmd1posD= NZrefIndxP(nonZeroMedPosIndx); %drfPindx((RFmd1posIndx),dMPs(mm));
RFmd1locD(1)= ceil(RFmd1posD/24); %calc r value
RFmd1locD(2)= RFmd1posD - ((RFmd1locD(1)-1)*24); %calc c value
lstindx=lstindx+1;
lstindxOrf= lstindxOrf+1;
if usrRefFg==0, rfPLbl= 'RF1mdP('; else rfPLbl= strcat('RF-',rfGnSp,'mdP('); end %accomodate User Ref Selection
if iscell(strcat(rfPLbl,num2str(d),')')),
aa(lstindx,1)= strcat(rfPLbl,num2str(d),')');
bb(lstindxOrf,1)= strcat(rfPLbl,num2str(d),')'); %remove string2cell brackets {...}
else
aa(lstindx,1)= {strcat(rfPLbl,num2str(d),')')};
bb(lstindxOrf,1)= {strcat(rfPLbl,num2str(d),')')}; %remove string2cell brackets {...}
end
aa(lstindx,2)= {strcat(':',num2str(dMPs(mm)),':',num2str(RFmd1locD(1)),':',num2str(RFmd1locD(2)))};
bb(lstindxOrf,2)={strcat(':',num2str(dMPs(mm)),':',num2str(RFmd1locD(1)),':',num2str(RFmd1locD(2)))};
Exp(expN).Dexp(n).RFmdPLB(d,dMPs(mm))= strcat(aa(lstindx,1),aa(lstindx,2));
Exp(expN).Dexp(n).RFmdPindx(d,dMPs(mm))= RFmd1posD;
Exp(expN).Dexp(n).RFmdPpltN(d,dMPs(mm))= dMPs(mm); %This is a storage of the MasterPlate used NOT the ScanPlate? WeMight wish to store the ScanPlateNumber also???
Exp(expN).Dexp(n).RFmdPscanN(d,dMPs(mm))=rf1scNdisp;
Exp(expN).Dexp(n).RFmedianP(d,dMPs(mm))= mval1Disp;
Exp(expN).Dexp(n).stdP(d,dMPs(mm))= std1Disp;
Exp(expN).Dexp(n).meanP(d,dMPs(mm))= mean1Disp;
Exp(expN).Dexp(n).minP(d,dMPs(mm))= minDisp;
Exp(expN).Dexp(n).maxP(d,dMPs(mm))= maxDisp;
else
% Need to set L r K values to zeros or pick the first spot with zeros
%Spot 1 could be other than zero as the median isn't calculated if fewer than some percent are nonzero
medianCalcFailedD= 'To Few nonZero spots for valid median RF1 selection'
firstZeroDindx= find(((Exp(expN).Dexp(n).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5))==0),1,'first');
firstZeroD= drfPindx((firstZeroDindx),dMPs(mm));
Exp(expN).Dexp(n).RFmdPindx(d,dMPs(mm))=firstZeroD;
Exp(expN).Dexp(n).RFmdPpltN(d,dMPs(mm))= dMPs(mm); %RF1mp; %Is this supposed to be the MP number or the ScanPlate number???
end %~isempty(NZrefIndxP) && length(medianIndxDisp) > 3 ln584
catch %try ln565
medianCalcTryFailed1D= 'Failed! Failed! Ln565 {Dispersed RF1s} "try" But process continued with placeholder Plate spot value!'
try
firstZeroindxD= find(vv((chgIndx(d):chgIndx(d+1)-1),5)==0,1,'first');
firstZeroPindx= uu(firstZeroindxD,4);
Exp(expN).Dexp(n).RFmdPpltN(d,dMPs(mm))= dMPs(mm);
Exp(expN).Dexp(n).RFmdPindx(d,dMPs(mm))=firstZeroPindx;
catch
catchissue='try at Ln565'
Exp(expN).Dexp(n).RFmdPpltN(d,dMPs(mm))= dMPs(mm);
Exp(expN).Dexp(n).RFmdPindx(d,dMPs(mm))=384; %if crapout,Then use spot384 as default to keep going
end
try
Exp(expN).Dexp(n).RFmdPpltN= dMPs(mm);
catch
catchissue='Ln619'
Exp(expN).Dexp(n).RFmdPpltN= 1; %This might keep from breaking BUT ???
end
error='EZexpSel lineAfter 565'
end %try ~ln565
end %for d=0:DMnum
end %for mm=1:length(dMPs)
%****************CALC. GLOBAL MEAN, STD, AND MEDIAN FOR DISTRIBUTED REFERENCES******************************************************************
uu= horzcat(uu,vv);
for d=1:DMnum
medianIndxG=[];
NZrfIndxG=[];
minG=min(nonzeros(vv(:,d)));
maxG=max(nonzeros(vv(:,d)));
RFmeanG= mean(nonzeros(vv(:,d)));
RFstdG= std(nonzeros(vv(:,d)));
NZrfIndxG= find(vv(:,d)); %find(nonzeros(vv(:,d)));
if isempty(RFmeanG), nonZeroCntD=0, %medianIndxDisp= RFmeanG(d);
else nonZeroCntD= length(nonzeros(vv(:,d)));
end
%Calc. of median requires an odd number of indx items
if ~isempty(NZrfIndxG) && mod(nonZeroCntD,2)==0, medianIndxD= NZrfIndxG(1:(size(NZrfIndxG,1)-1)); end
if ~isempty(NZrfIndxG) && mod(nonZeroCntD,2)~=0, medianIndxD= NZrfIndxG(:); end
if ~isempty(NZrfIndxG) && length(medianIndxD) > 0 %(.15*size(drf,1)) %To calc. a median, more than 15% of spots must be nonZero
mvalsDG= median(vv(medianIndxD,d)); %(nonzeros(vv(:,d)));
nzPosIndxDG=find(mvalsDG==vv(:,d));
RFmdDGloc(d,1)= uu(nzPosIndxDG,1); %MP of distributedGlobal Median value
RFmdDGloc(d,2)= uu(nzPosIndxDG,2); %calc r value
RFmdDGloc(d,3)= uu(nzPosIndxDG,3); %calc c value
lstindx=lstindx+1;
lstindxOrf= lstindxOrf+1;
if usrRefFg==0, rfGLbl= 'RF1mdG('; else rfGLbl= strcat('RF-',rfGnSp,'mdG('); end %accomodate User Ref Selection
if iscell(strcat(rfPLbl,num2str(d),')')),
aa(lstindx,1)= strcat(rfGLbl,num2str(d),')'); %remove string2cell brackets {...}
bb(lstindxOrf,1)= strcat(rfGLbl,num2str(d),')'); %remove string2cell brackets {...}
else
aa(lstindx,1)= {strcat(rfGLbl,num2str(d),')')};
bb(lstindxOrf,1)= {strcat(rfGLbl,num2str(d),')')};
end
aa(lstindx,2)= {strcat(':',num2str(RFmdDGloc(d,1)),':',num2str(RFmdDGloc(d,2)),':',num2str(RFmdDGloc(d,3)))}; %,'std_',num2str(std2))};
bb(lstindxOrf,2)= {strcat(':',num2str(RFmdDGloc(d,1)),':',num2str(RFmdDGloc(d,2)),':',num2str(RFmdDGloc(d,3)))}; %,'std_',num2str(std2))};
%Composite Reference Amalgum Plot ******************
lstindx=lstindx+1;
lstindxOrf= lstindxOrf+1;
if usrRefFg==0, rfcmpGLbl= 'RFcmpG('; else rfcmpGLbl= strcat('RFcmpG-',rfGnSp,'('); end %accomodate User Ref Selection
if iscell(strcat(rfcmpGLbl,num2str(d),')')),
aa(lstindx,1)= strcat(rfcmpGLbl,num2str(d),')'); %strcat('RFcmpG(',num2str(d),')');
bb(lstindxOrf,1)= strcat(rfcmpGLbl,num2str(d),')'); %strcat('RFcmpG(',num2str(d),')');
else
aa(lstindx,1)= {strcat(rfcmpGLbl,num2str(d),')')};
bb(lstindxOrf,1)= {strcat(rfcmpGLbl,num2str(d),')')};
end
aa(lstindx,2)={''};
bb(lstindxOrf,2)={''};
%*****************************************************
Exp(expN).Dexp(n).RFmdGLB(d)= strcat(aa(lstindx,1),aa(lstindx,2));
Exp(expN).Dexp(n).RFmdGindx(d)= nzPosIndxDG;
Exp(expN).Dexp(n).RFmdGpltN(d)= RFmdDGloc(d,1);
Exp(expN).Dexp(n).RFmdGscanN(d)= uu(nzPosIndxDG,4);
Exp(expN).Dexp(n).RFmedianG(d)= mvalsDG;
Exp(expN).Dexp(n).RFminG(d)= minG;
Exp(expN).Dexp(n).RFmaxG(d)= maxG;
Exp(expN).Dexp(n).RFstdG(d)= RFstdG;
Exp(expN).Dexp(n).RFmeanG(d)= RFmeanG;
Exp(expN).Dexp(n).RFcmpGL.dm(d).Lvals= vv(medianIndxD,d); %17_1201 TrendOL
Exp(expN).Dexp(n).RFcmpGL.dm(d).med= median(vv(medianIndxD,d)); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpGL.dm(d).mean= mean(vv(medianIndxD,d)); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpGL.dm(d).std= std(vv(medianIndxD,d)); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpGL.dm(d).min= min(vv(medianIndxD,d)); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpGL.dm(d).max= max(vv(medianIndxD,d)); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpGK.dm(d).Kvals= vvK(medianIndxD,d); %17_1201 TrendOL
Exp(expN).Dexp(n).RFcmpGK.dm(d).med= median(vvK(medianIndxD,d)); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpGK.dm(d).mean= mean(vvK(medianIndxD,d)); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpGK.dm(d).std= std(vvK(medianIndxD,d)); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpGK.dm(d).min= min(vvK(medianIndxD,d)); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpGK.dm(d).max= max(vvK(medianIndxD,d)); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpGr.dm(d).rvals= vvr(medianIndxD,d); %17_1201 TrendOL
Exp(expN).Dexp(n).RFcmpGr.dm(d).med= median(vvr(medianIndxD,d)); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpGr.dm(d).mean= mean(vvr(medianIndxD,d)); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpGr.dm(d).std= std(vvr(medianIndxD,d)); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpGr.dm(d).min= min(vvr(medianIndxD,d)); %For Ref Composite 17_1009
Exp(expN).Dexp(n).RFcmpGr.dm(d).max= max(vvr(medianIndxD,d)); %For Ref Composite 17_1009
end
end
end % if exist('drf','var')
%END OF DISPERSE REFERENCE PLATAES CALCULATIONS AND LIST ADDITIONS
%*********************************************************************
%Added 17-1023 For User Addition of Gene Composites to ListBox
%Expaa{expN,n}= aa; Expbb{expN,n}= bb;
%>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
%********************************************************************
%EZusrSelRef %*
%********************************************************************
%****************************************************************************************************
gnLstRaw= strcat(aa(:,1),aa(:,2));
Exp(expN).Dexp(n).srtGnLst= sort(gnLstRaw);
orfLstRaw=strcat(bb(:,1),bb(:,2));
Exp(expN).Dexp(n).srtOrfLst= sort(orfLstRaw);
%####################################################################
%
%{
%set(handles.MPsldr2,'max',length(MP));
%set(handles.DMsldr2,'max',length(DM.drug));
%set(handles.Tptsldr2,'max',tPtsSize);
%set(handles.MPsldr2,'min',1,'max',MPnum)
%set(handles.DMsldr2,'min',1,'max',DMnum)
%tPtsSize= size(Exp(expN).Dexp(n).FexpScanBMtp{1,1},(3));
%set(handles.Tptsldr2,'min',1,'max',tPtsSize)
%set(handles.MPsldr2,'value',1)
%set(handles.DMsldr2,'value',1)
%set(handles.Tptsldr2,'value',1)
%set(handles.MPed2,'string','1')
%set(handles.DMed2,'string','1')
%set(handles.Tpted2,'string','1')
%set(handles.MPsldr2,'SliderStep',[1/length(MP) 1/length(MP)]);
%set(handles.DMsldr2,'SliderStep',[1/length(DM.drug) 1/length(DM.drug)]);
%set(handles.Tptsldr2,'SliderStep',[1/tPtsSize 1/tPtsSize]);
%}
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