Nothing
R/wrapper.R
In RNAither: Statistical analysis of high-throughput RNAi screens
Defines functions
listChooseIndex
vennDiagfunc
function7
function6
function5
function4b
function4a
function3
function2
function1
gseaTableFunc
mainAnalysis
Documented in
mainAnalysis
mainAnalysis <- function(header, dataset, flagForSameExp, listOfNormalizations,
listOfArgs4norm, listOfStatTests, listOfArgs4stat, multTestAdj, hitScoringVec1,
hitScoringVec2, posNegFlag, flag4Gsea, vecOfChannels, whichOnto){
warning("The mainAnalysis() routine is deprecated. Please use rnaither() instead.")
firstLine<-strsplit(header[[1]], ",")
firstLineBis<-firstLine[[1]][2]
secondLine<-strsplit(header[[2]], ",")
secondLineBis<-secondLine[[1]][2]
thirdLine<-strsplit(header[[3]], "comments,")
thirdLineBis<-thirdLine[[1]][2]
#################################
##########QUALITY PLOTS##########
#################################
print(paste("Computing quality plots on raw data...", date(), sep=": "))
##MAINPAGE titles:
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file="index.html", quote=F, row.names=F, col.names=F)
write.table(paste("<BODY><CENTER><H1>", firstLineBis, "</H1></CENTER>", sep=""),
file="index.html", append=T, quote=F, row.names=F, col.names=F)
##SUBPAGE1 titles:
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file="sub1.html", quote=F, row.names=F, col.names=F)
write.table(paste("<BODY><CENTER><H2>Boxplots per Plate</H2></CENTER>", sep=""),
file="sub1.html", append=T, quote=F, row.names=F, col.names=F)
print(paste("Generating boxplots of signals...", date(), sep=": "))
function1(header, dataset, vecOfChannels, firstLineBis, secondLineBis,
"index.html", "sub1.html", 0)
print(paste("Generating spatial distribution of signals...", date(), sep=": "))
function2(header, dataset, vecOfChannels, firstLineBis, secondLineBis,
"index.html", "sub2.html", 0)
print(paste("Plotting signals per well...", date(), sep=": "))
function2b(header, dataset, vecOfChannels, firstLineBis, secondLineBis,
"index.html", "sub2b.html", 0)
if (length(vecOfChannels)>1){
print(paste("Comparing channels...", date(), sep=": "))
function2c(header, dataset, vecOfChannels, firstLineBis, secondLineBis,
"index.html", "sub2c.html", 0)
}
print(paste("Plotting histogram distribution of signals...", date(), sep=": "))
function3(header, dataset, vecOfChannels, posNegFlag, firstLineBis,
secondLineBis, "index.html", "sub3.html", 0)
print(paste("Plotting control densities...", date(), sep=": "))
function4a(header, dataset, vecOfChannels, posNegFlag, firstLineBis,
secondLineBis, "index.html", "sub4a.html", 0)
print(paste("Computing Z'factors...", date(), sep=": "))
function4b(header, dataset, vecOfChannels, posNegFlag, firstLineBis,
secondLineBis, "index.html", "sub4b.html", 0)
print(paste("Generating boxplots of control signals...", date(), sep=": "))
function5(header, dataset, vecOfChannels, posNegFlag, firstLineBis,
secondLineBis, "index.html", "sub5.html", 0)
print(paste("Generating QQ plots...", date(), sep=": "))
function6(header, dataset, vecOfChannels, firstLineBis, secondLineBis,
"index.html", "sub6.html", 0)
write.table("</BODY>", file="index.html", append=T, quote=F, row.names=F,
col.names=F)
write.table("</BODY>", file="sub1.html", append=T, quote=F, row.names=F,
col.names=F)
write.table("</BODY>", file="sub2.html", append=T, quote=F, row.names=F,
col.names=F)
write.table("</BODY>", file="sub2b.html", append=T, quote=F, row.names=F,
col.names=F)
write.table("</BODY>", file="sub2c.html", append=T, quote=F, row.names=F,
col.names=F)
write.table("</BODY>", file="sub3.html", append=T, quote=F, row.names=F,
col.names=F)
write.table("</BODY>", file="sub4a.html", append=T, quote=F, row.names=F,
col.names=F)
write.table("</BODY>", file="sub4b.html", append=T, quote=F, row.names=F,
col.names=F)
write.table("</BODY>", file="sub5.html", append=T, quote=F, row.names=F,
col.names=F)
write.table("</BODY>", file="sub6.html", append=T, quote=F, row.names=F,
col.names=F)
################################
##########NORMALIZATION#########
################################
print(paste("Normalizing data...", date(), sep=": "))
for (i in 1:length(listOfNormalizations)){
result<-listOfNormalizations[[i]](header, dataset, listOfArgs4norm[[i]])
header<-result[[1]]
dataset<-result[[2]]
##change Inf and -Inf values that potentially arise during normalization to NA
##it is IMPORTANT for this that the argument order for normalization functions stays the same!
col4plot<-listOfArgs4norm[[i]][[1]][1]
if(length(which(dataset[[get("col4plot")]]==Inf))>0){
places<-which(dataset[[get("col4plot")]]==Inf)
dataset[[get("col4plot")]][places]=NA
}
if(length(which(dataset[[get("col4plot")]]==-Inf))>0){
places<-which(dataset[[get("col4plot")]]==-Inf)
dataset[[get("col4plot")]][places]=NA
}
saveDataset(header, dataset, paste(firstLineBis, "_Fulldataset.txt", sep=""))
#################################
##########QUALITY PLOTS##########
#################################
print("Computing quality plots on normalized data...")
thirdLine<-strsplit(header[[3]], "comments,")
thirdLineBis<-thirdLine[[1]][2]
##MAINPAGE titles:
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file=paste("indexnorm", i, ".html", sep=""),
quote=F, row.names=F, col.names=F)
write.table(paste("<BODY><CENTER><H1>", firstLineBis, " after normalization",
"</H1></CENTER>", sep=""), file=paste("indexnorm", i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
write.table(paste("<CENTER>(", thirdLineBis, ")</CENTER>", sep=""),
file=paste("indexnorm", i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
##SUBPAGE1 titles:
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file=paste("sub1norm", i, ".html", sep=""),
quote=F, row.names=F, col.names=F)
write.table(paste("<BODY><CENTER><H1>Boxplots per Plate</H1></CENTER>", sep=""),
file=paste("sub1norm", i, ".html", sep=""), append=T, quote=F, row.names=F,
col.names=F)
print(paste("Generating boxplots of signals...", date(), sep=": "))
function1(header, dataset, vecOfChannels, firstLineBis, secondLineBis,
paste("indexnorm", i, ".html", sep=""), paste("sub1norm", i, ".html", sep=""),
i)
print(paste("Generating spatial distribution of signals...", date(), sep=": "))
function2(header, dataset, vecOfChannels, firstLineBis, secondLineBis,
paste("indexnorm", i, ".html", sep=""), paste("sub2norm", i, ".html", sep=""),
i)
print(paste("Plotting signals per well...", date(), sep=": "))
function2b(header, dataset, vecOfChannels, firstLineBis, secondLineBis,
paste("indexnorm", i, ".html", sep=""), paste("sub2bnorm", i, ".html", sep=""),
i)
if (length(vecOfChannels)>1){
print(paste("Comparing channels...", date(), sep=": "))
function2c(header, dataset, vecOfChannels, firstLineBis, secondLineBis,
paste("indexnorm", i, ".html", sep=""), paste("sub2cnorm", i, ".html", sep=""),
i)
}
print(paste("Plotting histogram distribution of signals...", date(), sep=": "))
function3(header, dataset, vecOfChannels, posNegFlag, firstLineBis,
secondLineBis, paste("indexnorm", i, ".html", sep=""),
paste("sub3norm", i, ".html", sep=""), i)
print(paste("Plotting control densities...", date(), sep=": "))
function4a(header, dataset, vecOfChannels, posNegFlag, firstLineBis,
secondLineBis, paste("indexnorm", i, ".html", sep=""),
paste("sub4anorm", i, ".html", sep=""), i)
print(paste("Computing Z'factors...", date(), sep=": "))
function4b(header, dataset, vecOfChannels, posNegFlag, firstLineBis,
secondLineBis, paste("indexnorm", i, ".html", sep=""),
paste("sub4bnorm", i, ".html", sep=""), i)
print(paste("Generating boxplots of control signals...", date(), sep=": "))
function5(header, dataset, vecOfChannels, posNegFlag, firstLineBis,
secondLineBis, paste("indexnorm", i, ".html", sep=""),
paste("sub5norm", i, ".html", sep=""), i)
print(paste("Generating QQ plots...", date(), sep=": "))
function6(header, dataset, vecOfChannels, firstLineBis, secondLineBis,
paste("indexnorm", i, ".html", sep=""), paste("sub6norm", i, ".html", sep=""),
i)
print(paste("Computing Spearman's correlation coefficients...", date(),
sep=": "))
function7(header, dataset, vecOfChannels, firstLineBis, secondLineBis,
paste("indexnorm", i, ".html", sep=""), paste("sub7anorm", i, ".html", sep=""),
paste("sub7bnorm", i, ".html", sep=""), flagForSameExp, i)
write.table("</BODY>", file=paste("indexnorm", i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
write.table("</BODY>", file=paste("sub1norm", i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
write.table("</BODY>", file=paste("sub2norm", i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
write.table("</BODY>", file=paste("sub2bnorm", i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
write.table("</BODY>", file=paste("sub2cnorm", i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
write.table("</BODY>", file=paste("sub3norm", i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
write.table("</BODY>", file=paste("sub4anorm", i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
write.table("</BODY>", file=paste("sub4bnorm", i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
write.table("</BODY>", file=paste("sub5norm", i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
write.table("</BODY>", file=paste("sub6norm", i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
write.table("</BODY>", file=paste("sub7anorm", i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
write.table("</BODY>", file=paste("sub7bnorm", i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
}
##############################
##########STAT TESTS##########
##############################
print(paste("Performing statistical tests...", date(), sep=": "))
##MAINPAGE titles:
write.table(paste("<HTML><HEAD><TITLE>Statistical analysis report, ",
secondLineBis, ", ", firstLineBis, "</TITLE></HEAD>", sep=""),
file="stats.html", quote=F, row.names=F, col.names=F)
##MAINPAGE Seitentitel:
write.table(paste("<BODY><CENTER><H1>Statistical analysis report, ",
firstLineBis, "</H1></CENTER>", sep=""), file="stats.html", append=T,
quote=F, row.names=F, col.names=F)
write.table(paste("<CENTER>(Normalizations performed: ", thirdLineBis,
")</CENTER>", sep=""), file="stats.html", append=T, quote=F,
row.names=F, col.names=F)
##Apply statistical tests and score hits:
hitVectors<-list("platzhalter")
hitVectorsTestNames<-list("platzhalter")
counterHitVectorsTestnames<-0
for (i in 1:length(listOfStatTests)){
testResult<-listOfStatTests[[i]](dataset, listOfArgs4stat[[i]])
pValVec<-testResult[[1]]
dataset<-testResult[[2]]
namepValVec<-testResult[[3]]
saveDataset(header, dataset, paste(firstLineBis, "_Fulldataset.txt", sep=""))
##adjust for multiple testing and reinsert pValVec into dataset:
pValVec<-multTestAdjust(pValVec, multTestAdj)
temp<-generateReplicateMat(dataset, 1, "Intensities", listOfArgs4stat[[i]][[3]],
listOfArgs4stat[[i]][[4]])
dataset<-incorporatepValVec(dataset, pValVec, temp[[1]],
listOfArgs4stat[[i]][[4]], paste(namepValVec, "_adjusted_", multTestAdj,
sep=""))
print(paste("Scoring hits...", date(), sep=": "))
result<-hitselectionPval(dataset, pValVec, listOfArgs4stat[[i]][[3]],
paste("hits_", namepValVec, "_adjusted_", multTestAdj, sep=""),
hitScoringVec2[1], listOfArgs4stat[[i]][[4]], paste("pval_hits_",
testResult[[4]], " (", i, ").txt", sep=""))
dataset<-result[[1]]
hitVectors[[i]]<-result[[2]]
hitVectorsTestNames[[i]]<-testResult[[4]]
hitThreshold<-round(result[[4]], digits=2)
if (hitScoringVec1[1] == 1){
##scoring according to only p-value
genesnPvals<-read.table(paste("pval_hits_", testResult[[4]], " (", i,
").txt", sep=""))
if (hitVectorsTestNames[[i]] == "Mann-Whitney test"
| hitVectorsTestNames[[i]] == "t test"){
if (listOfArgs4stat[[i]][[1]] == "g"){
upOrDownReg<-"Upregulated"
}
if (listOfArgs4stat[[i]][[1]] == "l"){
upOrDownReg<-"Downregulated"
}
if (listOfArgs4stat[[i]][[1]] == "two.sided"){
upOrDownReg<-"Up and downregulated"
}
}
if (hitVectorsTestNames[[i]] == "Rank product test"){
if (listOfArgs4stat[[i]][[2]] == 1){
upOrDownReg<-"Downregulated"
}
if (listOfArgs4stat[[i]][[2]] == 2){
upOrDownReg<-"Upregulated"
}
}
write.table(paste("<br><br><br><CENTER><H2>", upOrDownReg,
" genes according to ", hitVectorsTestNames[[i]],
"</H2> (multiple testing adjument: ", multTestAdj, ") (p-value < ",
hitThreshold, ") - <a href=\"", "pval_hits_", testResult[[4]], " (", i, ").txt",
"\">Textfile</a> -</CENTER>", sep=""), file="stats.html", append=T, quote=F,
row.names=F, col.names=F)
s1<-"<CENTER><TABLE border=0><TR><TH BGCOLOR=\"#d0d0f0\">Gene name</TH>"
s2<-"<TH BGCOLOR=\"#e0e0ff\">p-value</TH><TH BGCOLOR=\"#d0d0f0\">Median</TH>"
s3<-paste(s1, s2, sep="")
write.table(s3, file="stats.html", append=T, quote=F, row.names=F, col.names=F)
for (m in 1:(ncol(genesnPvals)-2)){
write.table("<TH BGCOLOR=\"#d0d0f0\">Norm val</TH>", file="stats.html",
append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
for (n in 1:nrow(genesnPvals)){
write.table(paste("<TR><TD BGCOLOR=\"#e0e0f0\">", rownames(genesnPvals)[n],
"</TD>", sep=""), file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
for (p in 1:ncol(genesnPvals)){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\" align=center>", genesnPvals[n, p],
"</TD>", sep=""), file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
}
write.table("</TR>", file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
}
write.table("</CENTER></TABLE>", file="stats.html", append=T, quote=F,
row.names=F, col.names=F)
##VOLCANO PLOT###
volcPlotName<-volcanoPlot(header, dataset, listOfArgs4stat[[i]][[3]],
paste(namepValVec, "_adjusted_", multTestAdj, sep=""),
listOfArgs4stat[[i]][[4]], paste("Volcano plot (", i, ")_p", sep=""),
hitScoringVec2[1], 0)
write.table("<br><br><CENTER>Volcano plot</CENTER><br>", file="stats.html",
append=T, quote=F, row.names=F, col.names=F)
write.table(paste("<CENTER><A HREF=\"", volcPlotName, ".pdf\"><IMG SRC=\"",
volcPlotName, ".png\"/></A></CENTER>", sep=""), file="stats.html", append=T,
quote=F, row.names=F, col.names=F)
##SPATIAL DISTRIBUTION OF HITS
res<-spatialDistribHits(header, dataset, paste("Spatial hits distribution (",
i, ")_p", sep=""), paste("hits_", namepValVec, "_adjusted_", multTestAdj,
sep=""), listOfArgs4stat[[i]][[4]], 0)
write.table("<BR><BR><CENTER><TABLE border=0><TR><TH BGCOLOR=\"#e0e0ff\"></TH>",
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
for (j in res[[3]][1]:res[[3]][2]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Plate ", j, "</TH>", sep=""),
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file="stats.html", append=T, quote=F, row.names=F, col.names=F)
for (k in res[[2]][1]:res[[2]][2]){
write.table(paste("<TR><TH BGCOLOR=\"#e0e0ff\">Exp. ", k, "</TH>", sep=""),
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
for (m in res[[3]][1]:res[[3]][2]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", res[[1]],
"_Exp_", k, "_Plate_", m, "_.html", "\"><IMG SRC=\"", res[[1]], "_Exp_", k,
"_Plate_", m, "_4html.png\"/></A></CENTER><BR></TD>", sep=""),
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
}
}
write.table("</TR></CENTER></TABLE>", file="stats.html", append=T, quote=F,
row.names=F, col.names=F)
}
if (hitScoringVec1[2] == 2 ){
##hitscoring according to zSc < thresh & pval < thresh in hitScoringVec2[1]
if (((hitVectorsTestNames[[i]] == "Mann-Whitney test"
| hitVectorsTestNames[[i]] == "t test")
& (listOfArgs4stat[[i]][[1]] == "two.sided"
| listOfArgs4stat[[i]][[1]] == "l"))
| (hitVectorsTestNames[[i]] == "Rank product test"
& listOfArgs4stat[[i]][[2]] == 1)){
result<-hitselectionZscorePval(dataset, pValVec, listOfArgs4stat[[i]][[3]],
paste("hits_", namepValVec, "_adjusted_", multTestAdj, "_ZScore<",
hitScoringVec2[2], sep=""), hitScoringVec2[2], hitScoringVec2[1], -2,
listOfArgs4stat[[i]][[4]], median, paste("pval_hits_", testResult[[4]],
"combined_ZSc_sm_", hitScoringVec2[2], ".txt", sep=""))
dataset<-result[[1]]
counterHitVectorsTestnames<-counterHitVectorsTestnames+1
hitVectors[[length(listOfStatTests)+counterHitVectorsTestnames]]<-result[[2]]
hitThresholdZsc<-round(result[[3]], digits=3)
hitThresholdPval<-round(result[[4]], digits=2)
s3<-paste(testResult[[4]], " & ZScore sm ", hitThresholdZsc, sep="")
hitVectorsTestNames[[length(listOfStatTests)+counterHitVectorsTestnames]]<-s3
genesnPvals<-read.table(paste("pval_hits_", testResult[[4]], "combined_ZSc_sm_",
hitScoringVec2[2], ".txt", sep=""))
upOrDownReg<-"Downregulated"
write.table(paste("<br><br><br><CENTER><H2>", upOrDownReg,
" genes according to ", hitVectorsTestNames[[length(listOfStatTests)
+counterHitVectorsTestnames]], "</H2> (multiple testing adjument: ",
multTestAdj, ") (Thresholds: pval < ", hitThresholdPval, ", Z-score < ",
hitThresholdZsc, ") - <a href=\"", "pval_hits_", testResult[[4]],
"combined_ZSc_sm_", hitScoringVec2[2], ".txt", "\">Textfile</a> -</CENTER>",
sep=""), file="stats.html", append=T, quote=F, row.names=F, col.names=F)
s5<-"<CENTER><TABLE border=0><TR><TH BGCOLOR=\"#d0d0f0\">Gene name</TH>"
s6<-"<TH BGCOLOR=\"#e0e0ff\">sumZScore</TH><TH BGCOLOR=\"#e0e0ff\">p-value</TH>"
s7<-paste(s5, s6, sep="")
write.table(s7, file="stats.html", append=T, quote=F, row.names=F, col.names=F)
for (m in 1:(ncol(genesnPvals)-2)){
write.table("<TH BGCOLOR=\"#d0d0f0\">Norm val</TH>", file="stats.html",
append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
for (n in 1:nrow(genesnPvals)){
write.table(paste("<TR><TD BGCOLOR=\"#e0e0f0\">", rownames(genesnPvals)[n],
"</TD>", sep=""), file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
for (p in 1:ncol(genesnPvals)){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\" align=center>",
genesnPvals[n, p], "</TD>", sep=""), file="stats.html", append=T,
quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
}
write.table("</CENTER></TABLE>", file="stats.html", append=T,
quote=F, row.names=F, col.names=F)
##VOLCANO PLOT###
if (hitScoringVec1[3] == 2){
volcPlotName<-volcanoPlot(header, dataset, listOfArgs4stat[[i]][[3]],
paste(namepValVec, "_adjusted_", multTestAdj, sep=""),
listOfArgs4stat[[i]][[4]], paste("Volcano plot (", i, ")_zl", sep=""),
c(hitScoringVec2[1], hitScoringVec2[2], hitScoringVec2[3]), 0)
}else{
volcPlotName<-volcanoPlot(header, dataset, listOfArgs4stat[[i]][[3]],
paste(namepValVec, "_adjusted_", multTestAdj, sep=""),
listOfArgs4stat[[i]][[4]], paste("Volcano plot (", i, ")_zl", sep=""),
c(hitScoringVec2[1], hitScoringVec2[2]), 0)
}
write.table("<br><br><CENTER>Volcano plot</CENTER><br>", file="stats.html",
append=T, quote=F, row.names=F, col.names=F)
write.table(paste("<CENTER><A HREF=\"", volcPlotName, ".pdf\"><IMG SRC=\"",
volcPlotName, ".png\"/></A></CENTER>", sep=""), file="stats.html",
append=T, quote=F, row.names=F, col.names=F)
res<-spatialDistribHits(header, dataset, paste("Spatial hits distribution (",
i, ")_zl", sep=""), paste("hits_", namepValVec, "_adjusted_", multTestAdj,
"_ZScore<", hitScoringVec2[2], sep=""), listOfArgs4stat[[i]][[4]], 0)
write.table("<BR><BR><CENTER><TABLE border=0><TR><TH BGCOLOR=\"#e0e0ff\"></TH>",
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
for (j in res[[3]][1]:res[[3]][2]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Plate ", j, "</TH>", sep=""),
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
for (k in res[[2]][1]:res[[2]][2]){
write.table(paste("<TR><TH BGCOLOR=\"#e0e0ff\">Exp. ", k, "</TH>", sep=""),
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
for (m in res[[3]][1]:res[[3]][2]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", res[[1]],
"_Exp_", k, "_Plate_", m, "_.html", "\"><IMG SRC=\"", res[[1]], "_Exp_", k,
"_Plate_", m, "_4html.png\"/></A></CENTER><BR></TD>", sep=""),
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
}
}
write.table("</TR></CENTER></TABLE>", file="stats.html", append=T,
quote=F, row.names=F, col.names=F)
}
}
if (hitScoringVec1[3] == 2){
##hitscoring according to zSc > thresh & pval < thresh in hitScoringVec2[1]
if (((hitVectorsTestNames[[i]] == "Mann-Whitney test"
| hitVectorsTestNames[[i]] == "t test")
& (listOfArgs4stat[[i]][[1]] == "two.sided"
| listOfArgs4stat[[i]][[1]] == "g"))
| (hitVectorsTestNames[[i]] == "Rank product test"
& listOfArgs4stat[[i]][[2]] == 2)){
result<-hitselectionZscorePval(dataset, pValVec, listOfArgs4stat[[i]][[3]],
paste("hits_", namepValVec, "_adjusted_", multTestAdj, "_ZScore>",
hitScoringVec2[3], sep=""), hitScoringVec2[3], hitScoringVec2[1], 2,
listOfArgs4stat[[i]][[4]], median, paste("pval_hits_", testResult[[4]],
"combined_ZSc_gr_", hitScoringVec2[3], ".txt", sep=""))
dataset<-result[[1]]
counterHitVectorsTestnames<-counterHitVectorsTestnames+1
hitVectors[[length(listOfStatTests)+counterHitVectorsTestnames]]<-result[[2]]
hitThresholdZsc<-round(result[[3]], digits=3)
hitThresholdPval<-round(result[[4]], digits=2)
hitVectorsTestNames[[length(listOfStatTests)+counterHitVectorsTestnames]]<-
paste(testResult[[4]], " & ZScore gr ", hitThresholdZsc, sep="")
genesnPvals<-read.table(paste("pval_hits_", testResult[[4]], "combined_ZSc_gr_",
hitScoringVec2[3], ".txt", sep=""))
upOrDownReg<-"Upregulated"
write.table(paste("<br><br><br><CENTER><H2>", upOrDownReg,
" genes according to ", hitVectorsTestNames[[length(listOfStatTests)
+counterHitVectorsTestnames]], "</H2> (multiple testing adjument: ",
multTestAdj, ") (Thresholds: p-value < ", hitThresholdPval, ", Z-score > ",
hitThresholdZsc, ") - <a href=\"", "pval_hits_", testResult[[4]],
"combined_ZSc_gr_", hitScoringVec2[3], ".txt", "\">Textfile</a> -</CENTER>",
sep=""), file="stats.html", append=T, quote=F, row.names=F, col.names=F)
s8<-"<CENTER><TABLE border=0><TR><TH BGCOLOR=\"#d0d0f0\">Gene name</TH>"
s9<-"<TH BGCOLOR=\"#e0e0ff\">sumZScore</TH><TH BGCOLOR=\"#e0e0ff\">p-value</TH>"
s1<-paste(s8, s9, sep="")
write.table(s1, file="stats.html", append=T, quote=F, row.names=F, col.names=F)
for (m in 1:(ncol(genesnPvals)-2)){
write.table("<TH BGCOLOR=\"#d0d0f0\">Norm val</TH>", file="stats.html",
append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
for (n in 1:nrow(genesnPvals)){
write.table(paste("<TR><TD BGCOLOR=\"#e0e0f0\">", rownames(genesnPvals)[n],
"</TD>", sep=""), file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
for (p in 1:ncol(genesnPvals)){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\" align=center>", genesnPvals[n, p],
"</TD>", sep=""), file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
}
write.table("</TR>", file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
}
write.table("</CENTER></TABLE>", file="stats.html", append=T, quote=F,
row.names=F, col.names=F)
##VOLCANO PLOT###
if (hitScoringVec1[3] == 2){
volcPlotName<-volcanoPlot(header, dataset, listOfArgs4stat[[i]][[3]],
paste(namepValVec, "_adjusted_", multTestAdj, sep=""),
listOfArgs4stat[[i]][[4]], paste("Volcano plot (", i, ")_zg", sep=""),
c(hitScoringVec2[1], hitScoringVec2[2], hitScoringVec2[3]), 0)
}else{
volcPlotName<-volcanoPlot(header, dataset, listOfArgs4stat[[i]][[3]],
paste(namepValVec, "_adjusted_", multTestAdj, sep=""),
listOfArgs4stat[[i]][[4]], paste("Volcano plot (", i, ")_zg", sep=""),
c(hitScoringVec2[1], hitScoringVec2[2]), 0)
}
write.table("<br><br><CENTER>Volcano plot</CENTER><br>", file="stats.html",
append=T, quote=F, row.names=F, col.names=F)
write.table(paste("<CENTER><A HREF=\"", volcPlotName, ".pdf\"><IMG SRC=\"",
volcPlotName, ".png\"/></A></CENTER>", sep=""), file="stats.html", append=T,
quote=F, row.names=F, col.names=F)
res<-spatialDistribHits(header, dataset, paste("Spatial hits distribution (",
i, ")_zg", sep=""), paste("hits_", namepValVec, "_adjusted_", multTestAdj,
"_ZScore>", hitScoringVec2[3], sep=""), listOfArgs4stat[[i]][[4]], 0)
write.table("<BR><BR><CENTER><TABLE border=0><TR><TH BGCOLOR=\"#e0e0ff\"></TH>",
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
for (j in res[[3]][1]:res[[3]][2]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Plate ", j, "</TH>", sep=""),
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
for (k in res[[2]][1]:res[[2]][2]){
write.table(paste("<TR><TH BGCOLOR=\"#e0e0ff\">Exp. ", k, "</TH>", sep=""),
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
for (m in res[[3]][1]:res[[3]][2]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", res[[1]],
"_Exp_", k, "_Plate_", m, "_.html", "\"><IMG SRC=\"", res[[1]], "_Exp_", k,
"_Plate_", m, "_4html.png\"/></A></CENTER><BR></TD>", sep=""),
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
}
}
write.table("</TR></CENTER></TABLE>", file="stats.html", append=T,
quote=F, row.names=F, col.names=F)
}
}
}
if (hitScoringVec1[2] == 1){
##scoring according to ZScore with ZScore <= threshold
result<-hitselectionZscore(dataset, "SigIntensity", "hits_ZScore_do",
hitScoringVec2[2], 2, -2, "GeneName", median, "ZScore_hits_smallerthresh.txt")
dataset<-result[[1]]
count<-length(hitVectors)
hitVectors[[count+1]]<-result[[2]]
hitVectorsTestNames[[count+1]]<-"ZScore_do"
hitThreshold<-round(result[[3]], digits=3)
res<-spatialDistribHits(header, dataset, "Spatial hits distribution (ZScore)",
"hits_ZScore_do", "GeneName", 0)
genesnPvals<-read.table("ZScore_hits_smallerthresh.txt")
write.table(paste("<br><br><br><CENTER><H2>Downregulated genes according to ",
hitVectorsTestNames[[count+1]], "</H2> (Threshold: Z-score < ", hitThreshold,
") - <a href=\"ZScore_hits_smallerthresh.txt\">Textfile</a> -</CENTER>",
sep=""), file="stats.html", append=T, quote=F, row.names=F, col.names=F)
s2<-"<CENTER><TABLE border=0><TR><TH BGCOLOR=\"#d0d0f0\">Gene name</TH>"
s3<-"<TH BGCOLOR=\"#e0e0ff\">ZScore (median)</TH>"
s4<-paste(s2, s3, sep="")
write.table(s4, file="stats.html", append=T, quote=F, row.names=F, col.names=F)
for (m in 1:(ncol(genesnPvals)-1)){
write.table("<TH BGCOLOR=\"#d0d0f0\">Norm val</TH>", file="stats.html",
append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
for (n in 1:nrow(genesnPvals)){
write.table(paste("<TR><TD BGCOLOR=\"#e0e0f0\">", rownames(genesnPvals)[n],
"</TD>", sep=""), file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
for (p in 1:ncol(genesnPvals)){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\" align=center>", genesnPvals[n, p],
"</TD>", sep=""), file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
}
write.table("</TR>", file="stats.html", append=T, quote=F,
row.names=F, col.names=F)
}
write.table("</CENTER></TABLE>", file="stats.html", append=T, quote=F,
row.names=F, col.names=F)
##SPATIAL DISTRIBUTION OF HITS - output
write.table("<BR><BR><CENTER><TABLE border=0><TR><TH BGCOLOR=\"#e0e0ff\"></TH>",
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
for (j in res[[3]][1]:res[[3]][2]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Plate ", j, "</TH>", sep=""),
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
for (k in res[[2]][1]:res[[2]][2]){
write.table(paste("<TR><TH BGCOLOR=\"#e0e0ff\">Exp. ", k, "</TH>", sep=""),
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
for (m in res[[3]][1]:res[[3]][2]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", res[[1]],
"_Exp_", k, "_Plate_", m, "_.html", "\"><IMG SRC=\"", res[[1]], "_Exp_", k,
"_Plate_", m, "_4html.png\"/></A></CENTER><BR></TD>", sep=""),
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
}
}
write.table("</TR></CENTER></TABLE>", file="stats.html", append=T, quote=F,
row.names=F, col.names=F)
}
if (hitScoringVec1[3] == 1){
result<-hitselectionZscore(dataset, "SigIntensity", "hits_ZScore_up",
hitScoringVec2[3], 2, 2, "GeneName", median, "ZScore_hits_higherthresh.txt")
dataset<-result[[1]]
count<-length(hitVectors)
hitVectors[[count+1]]<-result[[2]]
hitVectorsTestNames[[count+1]]<-"ZScore_up"
hitThreshold<-round(result[[3]], digits=3)
res<-spatialDistribHits(header, dataset, "Spatial hits distribution (ZScore)",
"hits_ZScore_up", "GeneName", 0)
genesnPvals<-read.table("ZScore_hits_higherthresh.txt")
write.table(paste("<br><br><br><CENTER><H2>Upregulated genes according to ",
hitVectorsTestNames[[count+1]], "</H2> (Threshold: Z-score >", hitThreshold,
") - <a href=\"ZScore_hits_higherthresh.txt\">Textfile</a> -</CENTER>", sep=""),
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
s6<-"<CENTER><TABLE border=0><TR><TH BGCOLOR=\"#d0d0f0\">Gene name</TH>"
s7<-"<TH BGCOLOR=\"#e0e0ff\">ZScore (median)</TH>"
s8<-paste(s6, s7, sep="")
write.table(s8, file="stats.html", append=T, quote=F, row.names=F, col.names=F)
for (m in 1:(ncol(genesnPvals)-1)){
write.table("<TH BGCOLOR=\"#d0d0f0\">Norm val</TH>", file="stats.html",
append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
for (n in 1:nrow(genesnPvals)){
write.table(paste("<TR><TD BGCOLOR=\"#e0e0f0\">", rownames(genesnPvals)[n],
"</TD>", sep=""), file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
for (p in 1:ncol(genesnPvals)){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\" align=center>", genesnPvals[n, p],
"</TD>", sep=""), file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
}
write.table("</TR>", file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
}
write.table("</CENTER></TABLE>", file="stats.html", append=T, quote=F,
row.names=F, col.names=F)
##SPATIAL DISTRIBUTION OF HITS - output
write.table("<BR><BR><CENTER><TABLE border=0><TR><TH BGCOLOR=\"#e0e0ff\"></TH>",
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
for (j in res[[3]][1]:res[[3]][2]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Plate ", j, "</TH>", sep=""),
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
for (k in res[[2]][1]:res[[2]][2]){
write.table(paste("<TR><TH BGCOLOR=\"#e0e0ff\">Exp. ", k, "</TH>", sep=""),
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
for (m in res[[3]][1]:res[[3]][2]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", res[[1]],
"_Exp_", k, "_Plate_", m, "_.html", "\"><IMG SRC=\"", res[[1]], "_Exp_", k,
"_Plate_", m, "_4html.png\"/></A></CENTER><BR></TD>", sep=""),
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
}
}
write.table("</TR></CENTER></TABLE>", file="stats.html", append=T, quote=F,
row.names=F, col.names=F)
}
blob<-vennDiagfunc(hitVectors, hitVectorsTestNames, hitScoringVec1,
listOfArgs4stat)
typeOfScoringVec<-blob[[1]]
typeOfComparison<-blob[[2]]
write.table("<br><br><br><CENTER><H2>Venn diagrams:</H2></CENTER><br>",
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><CENTER><TABLE border=0><TR>", file="stats.html", append=T,
quote=F, row.names=F, col.names=F)
for (element in c("l", "g", "two.sided")){
if (length(which(typeOfScoringVec == element))>1){
if (element == "l"){
write.table("<TH BGCOLOR=\"#e0e0ff\">Downregulated genes</TH>",
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
}
if (element == "g"){
write.table("<TH BGCOLOR=\"#e0e0ff\">Upregulated genes</TH>",
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
}
if (element == "two.sided"){
write.table("<TH BGCOLOR=\"#e0e0ff\">Up- and downregulated genes</TH>",
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
}
}
}
write.table("</TR><TR>", file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
##make the venn diagram plots:
for (element in c("l", "g", "two.sided")){
if (length(which(typeOfScoringVec == element))>1){
write.table("<TD BGCOLOR=\"#f0f0ff\"><CENTER><TABLE border=0><TR>",
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
for (compType in c("P", "Z", "PZ")){
if (length(which(typeOfComparison == compType
& typeOfScoringVec == element))>1){
arg4venn2<-as.list(hitVectorsTestNames[which(typeOfComparison == compType
& typeOfScoringVec == element)])
chosenScoringVecIndexes<-which((typeOfScoringVec == element)
& (typeOfComparison == compType))
arg4venn1<-listChooseIndex(hitVectors, chosenScoringVecIndexes)
if (length(arg4venn1) == 2 | length(arg4venn1) == 3){
vennPlotName<-vennDiag(header, arg4venn1, arg4venn2,
paste("Venn Diagram (", element, ") (", compType, ")", sep=""), 0)
write.table(paste("<TH><A HREF=\"", vennPlotName, ".pdf\"><IMG SRC=\"",
vennPlotName, ".png\"/></A></TH>", sep=""), file="stats.html", append=T,
quote=F, row.names=F, col.names=F)
}
}
}
write.table("</TD></TR></CENTER></TABLE>", file="stats.html", append=T,
quote=F, row.names=F, col.names=F)
}
}
write.table("</TR></CENTER></TABLE>", file="stats.html", append=T,
quote=F, row.names=F, col.names=F)
##LINK TO FULL DATASET:
saveDataset(header, dataset, paste(firstLineBis, "_Fulldataset.txt", sep=""))
write.table(paste("<br><br><br><CENTER><a href=\"", firstLineBis,
"_Fulldataset.txt\">Full scored dataset</a></CENTER><br>", sep=""),
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
##GSEA analysis
if(length(flag4Gsea)==1){
if(flag4Gsea==1){
print(paste("Performing GSEA analysis...", date(), sep=": "))
GOlist<-gseaAnalysisPt1(hitVectors[[1]], whichOnto)
for (g in 1:length(hitVectors)){
if (sum(hitVectors[[g]])>2 & sum(hitVectors[[g]])<length(hitVectors[[g]])){
geneTable<-gseaAnalysisPt2(hitVectors[[g]], GOlist, whichOnto)
write.table(geneTable, file=paste(firstLineBis, "_GSEAanalysis_",
hitVectorsTestNames[[g]], " (", typeOfScoringVec[[g]], ").txt", sep=""))
gseaTab<-read.table(paste(firstLineBis, "_GSEAanalysis_",
hitVectorsTestNames[[g]], " (", typeOfScoringVec[[g]], ").txt", sep=""))
gseaTableFunc(gseaTab, paste(firstLineBis, "_GSEAanalysis_",
hitVectorsTestNames[[g]], " (", typeOfScoringVec[[g]], ").txt", sep=""),
paste("Results of GSEA analysis for ", hitVectorsTestNames[[g]], " (",
typeOfScoringVec[[g]], ")", sep=""), paste("subGSEA", g, ".html", sep=""))
write.table(paste("<br><CENTER><a href=\"subGSEA", g,
".html\">Results of GSEA analysis for ", hitVectorsTestNames[[g]], " (",
typeOfScoringVec[[g]], ")</a></CENTER>", sep=""), file="stats.html",
append=T, quote=F, row.names=F, col.names=F)
}
}
}
}else{
print(paste("Performing GSEA analysis...", date(), sep=": "))
GOlist<-gseaAnalysisPt1(hitVectors[[1]], whichOnto)
for(i in 1:length(listOfStatTests)){
for (j in 1:length(hitScoringVec1)){
if(hitScoringVec1[j]>0){
indexNum<-(3-length(which(hitScoringVec1==0)))
g<-(j+(i-1)*indexNum)
if (flag4Gsea[g]==1 & sum(hitVectors[[g]])>2 & sum(hitVectors[[g]])<length(hitVectors[[g]])){
geneTable<-gseaAnalysisPt2(hitVectors[[g]], GOlist, whichOnto)
write.table(geneTable, file=paste(firstLineBis, "_GSEAanalysis_",
hitVectorsTestNames[[g]], " (", typeOfScoringVec[[g]], ").txt", sep=""))
gseaTab<-read.table(paste(firstLineBis, "_GSEAanalysis_",
hitVectorsTestNames[[g]], " (", typeOfScoringVec[[g]], ").txt", sep=""))
gseaTableFunc(gseaTab, paste(firstLineBis, "_GSEAanalysis_",
hitVectorsTestNames[[g]], " (", typeOfScoringVec[[g]], ").txt", sep=""),
paste("Results of GSEA analysis for ", hitVectorsTestNames[[g]], " (",
typeOfScoringVec[[g]], ")", sep=""), paste("subGSEA", g, ".html", sep=""))
write.table(paste("<br><CENTER><a href=\"subGSEA", g,
".html\">Results of GSEA analysis for ", hitVectorsTestNames[[g]], " (",
typeOfScoringVec[[g]], ")</a></CENTER>", sep=""), file="stats.html",
append=T, quote=F, row.names=F, col.names=F)
}
}
}
}
}
write.table("</BODY>", file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
s1<-"Analysis finished. Quality analysis of raw data can be found in index.html"
s2<-", quality analysis of normalized data can be found in indexnorm.html. "
s3<-"Statistical analysis can be found in stats.html. "
s4<-date()
print(paste(s1, s2, s3, s4, sep=""))
}
gseaTableFunc<-function(gseaTab, gseaTabfile, gseaTitle, nameOfHtmlPage){
write.table(paste("<BR><BR><CENTER><H2>", gseaTitle, "</H2><a href=\"",
gseaTabfile, "\">Textfile</a></CENTER><br><br><CENTER><TABLE border=0><TR>",
sep=""), file=nameOfHtmlPage, quote=F, row.names=F, col.names=F)
for (i in 1:length(colnames(gseaTab))){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">", colnames(gseaTab)[i], "</TH>",
sep=""), file=nameOfHtmlPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=nameOfHtmlPage, append=T, quote=F, row.names=F,
col.names=F)
for (j in 1:nrow(gseaTab)){
write.table("<TR>", file=nameOfHtmlPage, append=T, quote=F, row.names=F,
col.names=F)
for (k in 1:ncol(gseaTab)){
write.table(paste("<TD BGCOLOR=\"#e0e0f0\">", gseaTab[j, k], "</TD>", sep=""),
file=nameOfHtmlPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=nameOfHtmlPage, append=T, quote=F, row.names=F,
col.names=F)
}
write.table("</TABLE></CENTER>", file=nameOfHtmlPage, append=T, quote=F,
row.names=F, col.names=F)
}
function1<-function(header, dataset, vecOfChannels, firstLineBis, secondLineBis, indexOutput, subPage, flag){
#########
####1####
#########
write.table("<BR><BR><CENTER><TABLE border=0><TR>", file=subPage, append=T,
quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subPage, append=T, quote=F, row.names=F,
col.names=F)
write.table("<TR>", file=subPage, append=T, quote=F, row.names=F,
col.names=F)
for (i in 1:length(vecOfChannels)){
if (flag == 0){
namePlot1<-makeBoxplotPerScreen(header, dataset, vecOfChannels[i],
paste("Data (", i, ") per Exp.", sep=""), 0)
}else{
namePlot1<-makeBoxplotPerScreen(header, dataset, vecOfChannels[i],
paste("norm. Data (", flag, ") (", i, ") per Exp.", sep=""), 0)
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"",
namePlot1, ".pdf\"><IMG SRC=\"", namePlot1, ".png\"/></A></CENTER><BR></TD>",
sep=""), file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subPage, append=T, quote=F, row.names=F,
col.names=F)
for (i in 1:length(vecOfChannels)){
if (flag == 0){
stuff<-makeBoxplotPerPlate(header, dataset, vecOfChannels[i],
paste("Data (", i, ") per Plate", sep=""), 2, 0)
}else{
stuff<-makeBoxplotPerPlate(header, dataset, vecOfChannels[i],
paste("norm. Data (", flag, ") (", i, ") per Plate", sep=""), 2, 0)
}
s1<-"<BR><BR><CENTER><TABLE border=0><TR><TD BGCOLOR=\"#e0e0f0\"><H3 align="
s2<-"left>Channel"
s3<-"</H3></TD>"
write.table(paste(s1, s2, i, s3, sep=""), file=subPage, append=T,
quote=F, row.names=F, col.names=F)
for (j in stuff[[2]]:stuff[[3]]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"",
stuff[[1]], "(Exp. ", j, ").pdf\"><IMG SRC=\"", stuff[[1]], "(Exp. ", j,
").png\"/></A></CENTER><BR></TD>", sep=""), file=subPage, append=T,
quote=F, row.names=F, col.names=F)
}
}
for (i in 1:length(vecOfChannels)){
if (flag == 0){
stuff<-makeBoxplot4PlateType(header, dataset, vecOfChannels[i],
paste("Data (", i, ") per Exp.", sep=""), 0)
}else{
stuff<-makeBoxplot4PlateType(header, dataset, vecOfChannels[i],
paste("norm. Data (", flag, ") (", i, ") per Exp.", sep=""), 0)
}
s4<-"<BR><BR><CENTER><TABLE border=0><TR><TD BGCOLOR=\"#e0e0f0\"><H3 align=left"
s5<-">Channel"
s6<-"</H3></TD>"
write.table(paste(s4, s5, i, s6, sep=""), file=subPage, append=T, quote=F,
row.names=F, col.names=F)
for (j in stuff[[2]]:stuff[[3]]){ #for each plate type / for each plot
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"",
stuff[[1]], " for Plate", j, ".pdf\"><IMG SRC=\"", stuff[[1]],
" for Plate", j, ".png\"/></A></CENTER><BR></TD>", sep=""), file=subPage,
append=T, quote=F, row.names=F, col.names=F)
}
}
write.table("<BR><BR><CENTER><TABLE border=0><TR>", file=indexOutput,
append=T, quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
write.table("<TR>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
for (i in 1:length(vecOfChannels)){
if (flag == 0){
namePlot1<-makeBoxplotPerScreen(header, dataset, vecOfChannels[i],
paste("Data (", i, ") per Exp.", sep=""), 0)
}else{
namePlot1<-makeBoxplotPerScreen(header, dataset, vecOfChannels[i],
paste("norm. Data (", flag, ") (", i, ") per Exp.", sep=""), 0)
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", subPage,
"\"><IMG SRC=\"", namePlot1, ".png\"/></A></CENTER><BR></TD>", sep=""),
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=indexOutput, append=T,
quote=F, row.names=F, col.names=F)
}
function2<-function(header, dataset, vecOfChannels, firstLineBis,
secondLineBis, indexOutput, subPage, flag){
#########
####2####
#########
s1<-"<br><br><br><CENTER><H2>Spatial distribution of Intensities</H2></CENTER>"
write.table(s1, file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
if (flag == 0){
stuff2<-spatialDistrib(header, dataset, paste("Spatial I distribution (", i,
")", sep=""), vecOfChannels[i], "Internal_GeneID", 0)
}else{
stuff2<-spatialDistrib(header, dataset, paste("norm. Spatial I distribution (",
flag, ") (", i, ")", sep=""), vecOfChannels[i], "Internal_GeneID", 0)
}
if (i>1){
write.table("<BR>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
}
s2<-"<BR><CENTER><TABLE border=0><TR><TH BGCOLOR=\"#e0e0ff\">Channel "
write.table(paste(s2, i, "</TH>", sep=""), file=indexOutput, append=T,
quote=F, row.names=F, col.names=F)
for (j in stuff2[[3]][1]:stuff2[[3]][2]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Plate ", j, "</TH>", sep=""),
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
for (k in stuff2[[2]][1]:stuff2[[2]][2]){
write.table(paste("<TR><TH BGCOLOR=\"#e0e0ff\">Exp. ", k, "</TH>", sep=""),
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
for (m in stuff2[[3]][1]:stuff2[[3]][2]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", stuff2[[1]],
"_Exp_", k, "_Plate_", m, "_.html", "\"><IMG SRC=\"", stuff2[[1]], "_Exp_", k,
"_Plate_", m, "_4html.png\"/></A></CENTER><BR></TD>", sep=""), file=indexOutput,
append=T, quote=F, row.names=F, col.names=F)
}
}
write.table("</TR></CENTER></TABLE>", file=indexOutput, append=T, quote=F,
row.names=F, col.names=F)
}
s4<-"<br><br><br><CENTER><H2>Standard deviation of Intensities</H2></CENTER>"
write.table(s4, file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><CENTER><TABLE border=0><TR>", file=indexOutput, append=T,
quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=indexOutput, append=T, quote=F,
row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
if (flag == 0){
zeugs<-compareReplicateSD(header, dataset, paste("SD (", i, ") of replicates",
sep=""), vecOfChannels[i], "GeneName", 0)
}else{
zeugs<-compareReplicateSD(header, dataset, paste("SD (", i,
") of norm. replicates (", flag, ")", sep=""), vecOfChannels[i], "GeneName", 0)
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", subPage,
"\"><IMG SRC=\"", zeugs, " 4html.png\"/></A></CENTER><BR></TD>", sep=""),
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=indexOutput, append=T, quote=F,
row.names=F, col.names=F)
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file=subPage, quote=F, row.names=F, col.names=F)
s1<-"<CENTER><H2>Standard deviation of Intensities per experiment</H2></CENTER>"
write.table(s1, file=subPage, append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><BR><CENTER><TABLE border=0><TR>", file=subPage, append=T,
quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subPage, append=T, quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
if (flag == 0){
zeugs<-compareReplicateSD(header, dataset, paste("SD (", i, ") of replicates",
sep=""), vecOfChannels[i], "GeneName", 0)
}else{
zeugs<-compareReplicateSD(header, dataset, paste("SD (", i,
") of norm. replicates (", flag, ")", sep=""), vecOfChannels[i], "GeneName", 0)
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", zeugs,
" .html\"><IMG SRC=\"", zeugs, " 4html.png\"/></A></CENTER><BR></TD>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=subPage, append=T, quote=F,
row.names=F, col.names=F)
write.table(paste("<BR><BR><CENTER><TABLE border=0><TR>", sep=""), file=subPage,
append=T, quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
write.table("<TH BGCOLOR=\"#e0e0ff\"></TH>", file=subPage, append=T,
quote=F, row.names=F, col.names=F)
if (flag == 0){
stuff<-compareReplicateSDPerScreen(header, dataset, paste("SD (", i,
") of replicates", sep=""), vecOfChannels[i], "GeneName", 0)
}else{
stuff<-compareReplicateSDPerScreen(header, dataset, paste("SD (", i,
") of norm. replicates (", flag, ")", sep=""), vecOfChannels[i], "GeneName", 0)
}
for (j in stuff[[2]]:stuff[[3]]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Exp. ", j, "</TH>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subPage, append=T, quote=F, row.names=F, col.names=F)
write.table(paste("<TR><TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
for (j in stuff[[2]]:stuff[[3]]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", stuff[[1]],
"_Exp_", j, "_.html\"><IMG SRC=\"", stuff[[1]], "_Exp_", j,
"_4html.png\"/></A></CENTER><BR></TD>", sep=""), file=subPage, append=T,
quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</CENTER></TABLE>", file=subPage, append=T, quote=F,
row.names=F, col.names=F)
}
function2b <-function (header, dataset, vecOfChannels,
firstLineBis, secondLineBis, indexOutput, subPage, flag){
##########
####2b####
##########
subPageClip1<-strsplit(subPage, ".html")
subPageClip<-subPageClip1[[1]][1]
subPageClip<-paste(subPageClip, "_", sep="")
s1<-"<BR><BR><BR><CENTER><H2>Distribution of data per well</H2></CENTER>"
write.table(s1, sep="", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
numOfScreens<-max(dataset$ScreenNb)
minOfScreens<-min(dataset$ScreenNb)
write.table(paste("<BR><BR><CENTER>", sep=""), file=indexOutput,
append=T, quote=F, row.names=F, col.names=F)
for (i in minOfScreens:numOfScreens){
write.table(paste("<A HREF=\"", subPageClip, i, ".html\">Experiment ",
i, "</A><br>", sep=""), file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file=paste(subPageClip, i, ".html", sep=""),
quote=F, row.names=F, col.names=F)
for (o in 1:length(vecOfChannels)){
if (flag == 0){
stuff2<-ZScorePlotTwo(header, dataset, 2, 1, vecOfChannels[o],
"GeneName", paste("Data per well (", o, ")", sep=""), 0)
}else{
stuff2<-ZScorePlotTwo(header, dataset, 2, 1, vecOfChannels[o], "GeneName",
paste("norm. Data per well (", flag, ") (", o, ")", sep=""), 0)
}
write.table(paste("<BR><BR><CENTER><TABLE border=0><TR>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
write.table("<TH BGCOLOR=\"#e0e0ff\"></TH>", file=paste(subPageClip, i,
".html", sep=""), append=T, quote=F, row.names=F, col.names=F)
for (j in stuff2[[3]][1]:stuff2[[3]][2]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Plate ", j, "</TH>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
}
write.table("</TR>", file=paste(subPageClip, i, ".html", sep=""), append=T,
quote=F, row.names=F, col.names=F)
write.table(paste("<TR><TH BGCOLOR=\"#e0e0ff\">Channel ", o, "</TH>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F, row.names=F,
col.names=F)
for (j in stuff2[[3]][1]:stuff2[[3]][2]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", stuff2[[1]],
"_Exp_", i, "_Plate_", j, "_.pdf\"><IMG SRC=\"", stuff2[[1]], "_Exp_", i,
"_Plate_", j, "_.png\"/></A></CENTER><BR></TD>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
}
}
write.table(paste("</CENTER>", sep=""), file=indexOutput, append=T, quote=F,
row.names=F, col.names=F)
}
function2c <-function (header, dataset, vecOfChannels, firstLineBis,
secondLineBis, indexOutput, subPage, flag){
##########
####2c####
##########
subPageClip1<-strsplit(subPage, ".html")
subPageClip<-subPageClip1[[1]][1]
subPageClip<-paste(subPageClip, "_", sep="")
combinationNum<-choose(length(vecOfChannels), 2)
write.table("<BR><BR><BR><CENTER><H2>Comparison of channels</H2></CENTER>",
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><CENTER><TABLE border=0><TR>", file=indexOutput, append=T,
quote=F, row.names=F, col.names=F)
if (flag == 0){
zeugs<-channelPlot(header, dataset, vecOfChannels, 0, "Channel comparison", 0)
}else{
zeugs<-channelPlot(header, dataset, vecOfChannels, 0,
paste("Channel comparison (", flag, ")", sep=""), 0)
}
for (i in 1:length(combinationNum)){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", subPage,
"\"><IMG SRC=\"", zeugs, "(", i, ").png\"/></A></CENTER><BR></TD>", sep=""),
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=indexOutput, append=T, quote=F,
row.names=F, col.names=F)
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file=subPage, quote=F, row.names=F, col.names=F)
write.table("<CENTER><H2>Comparison of channels - per experiment</H2></CENTER>",
file=subPage, append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><BR><CENTER><TABLE border=0><TR>", file=subPage, append=T,
quote=F, row.names=F, col.names=F)
if (flag == 0){
zeugs<-channelPlot(header, dataset, vecOfChannels, 0, "Channel comparison", 0)
}else{
zeugs<-channelPlot(header, dataset, vecOfChannels, 0,
paste("Channel comparison (", flag, ")", sep=""), 0)
}
for (i in 1:length(combinationNum)){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", zeugs, "(", i,
").pdf\"><IMG SRC=\"", zeugs, "(", i, ").png\"/></A></CENTER><BR></TD>",
sep=""), file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=subPage, append=T, quote=F,
row.names=F, col.names=F)
if (flag == 0){
stuff<-channelPlot(header, dataset, vecOfChannels, 1, "Channel comparison", 0)
}else{
stuff<-channelPlot(header, dataset, vecOfChannels, 1,
paste("Channel comparison (", flag, ")", sep=""), 0)
}
write.table(paste("<BR><BR><CENTER><TABLE border=0><TR>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
for (j in stuff[[2]]:stuff[[3]]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Exp. ", j, "</TH>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subPage, append=T, quote=F, row.names=F,
col.names=F)
for (i in 1:length(combinationNum)){
write.table(paste("<TR>", sep=""), file=subPage, append=T, quote=F,
row.names=F, col.names=F)
for (j in stuff[[2]]:stuff[[3]]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", subPageClip, j,
".html\"><IMG SRC=\"", stuff[[1]], "(", i, ") (Exp. ", j,
").png\"/></A></CENTER><BR></TD>", sep=""), file=subPage, append=T, quote=F,
row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=subPage, append=T, quote=F,
row.names=F, col.names=F)
}
for (i in stuff[[2]]:stuff[[3]]){
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file=paste(subPageClip, i, ".html", sep=""),
quote=F, row.names=F, col.names=F)
s1<-"<CENTER><H2>Comparison of channels - per plate for experiment "
s2<-"</H2></CENTER>"
write.table(paste(s1, i, s2, sep=""), file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><BR><CENTER><TABLE border=0><TR>", file=paste(subPageClip, i,
".html", sep=""), append=T, quote=F, row.names=F, col.names=F)
if (flag == 0){
zeugs<-channelPlot(header, dataset, vecOfChannels, 1, "Channel comparison", 0)
}else{
zeugs<-channelPlot(header, dataset, vecOfChannels, 1,
paste("Channel comparison (", flag, ")", sep=""), 0)
}
for (j in 1:length(combinationNum)){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", zeugs[[1]], "(",
j, ") (Exp. ", i, ").pdf\"><IMG SRC=\"", zeugs[[1]], "(", j, ") (Exp. ", i,
").png\"/></A></CENTER><BR></TD>", sep=""), file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
if (flag == 0){
stuff2<-channelPlot(header, dataset, vecOfChannels, 2, "Channel comparison", 0)
}else{
stuff2<-channelPlot(header, dataset, vecOfChannels, 2,
paste("Channel comparison (", flag, ")", sep=""), 0)
}
write.table(paste("<BR><BR><CENTER><TABLE border=0><TR>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
for (j in stuff2[[3]][1]:stuff2[[3]][2]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Plate", j, "</TH>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
}
write.table(paste("</TR>", sep=""), file=paste(subPageClip, i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
for (o in 1:length(combinationNum)){
write.table(paste("<TR>", sep=""), file=paste(subPageClip, i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
for (j in stuff2[[3]][1]:stuff2[[3]][2]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", stuff2[[1]],
"(", o, ")_Exp_", i, "_Plate_", j, "_.pdf\"><IMG SRC=\"", stuff2[[1]], "(", o,
")_Exp_", i, "_Plate_", j, "_.png\"/></A></CENTER><BR></TD>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F, row.names=F,
col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
}
}
}
function3<-function(header, dataset, vecOfChannels, posNegFlag, firstLineBis,
secondLineBis, indexOutput, subPage, flag){
#########
####3####
#########
subPageClip1<-strsplit(subPage, ".html")
subPageClip<-subPageClip1[[1]][1]
subPageClip<-paste(subPageClip, "_", sep="")
write.table("<BR><BR><BR><CENTER><H2>Distribution of data</H2></CENTER>",
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><CENTER><TABLE border=0><TR>", file=indexOutput, append=T,
quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
write.table("<TR>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
for (i in 1:length(vecOfChannels)){
if (posNegFlag == 0){
if (flag == 0){
zeugs<-plotHisto(header, dataset, vecOfChannels[i],
paste("Distribution of Data (", i, ")", sep=""), 0)
}else{
zeugs<-plotHisto(header, dataset, vecOfChannels[i],
paste("Distribution of norm. Data (", flag, ") (", i, ")", sep=""), 0)
}
}else{
if (flag == 0){
zeugs<-plotControlHisto(header, dataset, vecOfChannels[i],
paste("Distribution of Data and Controls (", i, ")", sep=""), 0)
}else{
zeugs<-plotControlHisto(header, dataset, vecOfChannels[i],
paste("Distribution of norm. Data (", flag, ") and Controls (", i, ")",
sep=""), 0)
}
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", subPage,
"\"><IMG SRC=\"", zeugs, ".png\"/></A></CENTER><BR></TD>", sep=""),
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=indexOutput, append=T,
quote=F, row.names=F, col.names=F)
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file=subPage, quote=F, row.names=F, col.names=F)
write.table("<CENTER><H2>Distribution of data per experiment</H2></CENTER>",
file=subPage, append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><BR><CENTER><TABLE border=0><TR>", file=subPage, append=T,
quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subPage, append=T, quote=F, row.names=F, col.names=F)
write.table("<TR>", file=subPage, append=T, quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
if (posNegFlag == 0){
if (flag == 0){
zeugs<-plotHisto(header, dataset, vecOfChannels[i],
paste("Distribution of Data (", i, ")", sep=""), 0)
}else{
zeugs<-plotHisto(header, dataset, vecOfChannels[i],
paste("Distribution of norm. Data (", flag, ") (", i, ")", sep=""), 0)
}
}else{
if (flag == 0){
zeugs<-plotControlHisto(header, dataset, vecOfChannels[i],
paste("Distribution of Data and Controls (", i, ")", sep=""), 0)
}else{
zeugs<-plotControlHisto(header, dataset, vecOfChannels[i],
paste("Distribution of norm. Data (", flag, ") and Controls (", i,
")", sep=""), 0)
}
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", zeugs,
".pdf\"><IMG SRC=\"", zeugs, ".png\"/></A></CENTER><BR></TD>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=subPage, append=T, quote=F,
row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
if (posNegFlag == 0){
if (flag == 0){
stuff<-plotHistoPerscreen(header, dataset, vecOfChannels[i],
paste("Distribution of Data (", i, ")", sep=""), 2, 0)
}else{
stuff<-plotHistoPerscreen(header, dataset, vecOfChannels[i],
paste("Distribution of norm. Data (", flag, ") (", i, ")", sep=""), 2, 0)
}
}else{
if (flag == 0){
stuff<-plotControlHistoPerscreen(header, dataset, vecOfChannels[i],
paste("Distribution of Data and Controls (", i, ")", sep=""), 2, 0)
}else{
stuff<-plotControlHistoPerscreen(header, dataset, vecOfChannels[i],
paste("Distribution of norm. Data (", flag, ") and Controls (", i, ")",
sep=""), 2, 0)
}
}
write.table(paste("<BR><BR><CENTER><TABLE border=0><TR>", sep=""), file=subPage,
append=T, quote=F, row.names=F, col.names=F)
write.table("<TH BGCOLOR=\"#e0e0ff\"></TH>", file=subPage, append=T, quote=F,
row.names=F, col.names=F)
for (j in stuff[[2]]:stuff[[3]]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Exp. ", j, "</TH>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subPage, append=T, quote=F, row.names=F, col.names=F)
write.table(paste("<TR><TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
for (j in stuff[[2]]:stuff[[3]]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", subPageClip, j,
".html\"><IMG SRC=\"", stuff[[1]], "(Exp. ", j,
").png\"/></A></CENTER><BR></TD>", sep=""), file=subPage, append=T,
quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=subPage, append=T, quote=F,
row.names=F, col.names=F)
}
for (i in stuff[[2]]:stuff[[3]]){
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file=paste(subPageClip, i, ".html", sep=""),
quote=F, row.names=F, col.names=F)
write.table(paste("<CENTER><H2>Distribution of data per plate for experiment ",
i, "</H2></CENTER>", sep=""), file=paste(subPageClip, i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><BR><CENTER><TABLE border=0><TR>", file=paste(subPageClip, i,
".html", sep=""), append=T, quote=F, row.names=F, col.names=F)
for (j in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", j, "</TH>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
}
write.table("</TR>", file=paste(subPageClip, i, ".html", sep=""), append=T,
quote=F, row.names=F, col.names=F)
write.table("<TR>", file=paste(subPageClip, i, ".html", sep=""), append=T,
quote=F, row.names=F, col.names=F)
for (j in 1:length(vecOfChannels)){
if (posNegFlag == 0){
if (flag == 0){
zeugs<-plotHistoPerscreen(header, dataset, vecOfChannels[j],
paste("Distribution of Data (", j, ")", sep=""), 2, 0)
}else{
zeugs<-plotHistoPerscreen(header, dataset, vecOfChannels[j],
paste("Distribution of norm. Data (", flag, ") (", j, ")", sep=""), 2, 0)
}
}else{
if (flag == 0){
zeugs<-plotControlHistoPerscreen(header, dataset, vecOfChannels[j],
paste("Distribution of Data and Controls (", j, ")", sep=""), 2, 0)
}else{
zeugs<-plotControlHistoPerscreen(header, dataset, vecOfChannels[j],
paste("Distribution of norm. Data (", flag, ") and Controls (", j, ")",
sep=""), 2, 0)
}
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", zeugs[[1]],
"(Exp. ", i, ").pdf\"><IMG SRC=\"", zeugs[[1]], "(Exp. ", i,
").png\"/></A></CENTER><BR></TD>", sep=""), file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
for (o in 1:length(vecOfChannels)){
if (posNegFlag == 0){
if (flag == 0){
stuff2<-plotHistoPerplate(header, dataset, vecOfChannels[o],
paste("Distribution of Data (", o, ")", sep=""), 2, 0)
}else{
stuff2<-plotHistoPerplate(header, dataset, vecOfChannels[o],
paste("Distribution of norm. Data (", flag, ") (", o, ")", sep=""), 2, 0)
}
}else{
if (flag == 0){
stuff2<-plotControlHistoPerplate(header, dataset, vecOfChannels[o],
paste("Distribution of Data and Controls (", o, ")", sep=""), 2, 0)
}else{
stuff2<-plotControlHistoPerplate(header, dataset, vecOfChannels[o],
paste("Distribution of norm. Data (", flag, ") and Controls (", o, ")",
sep=""), 2, 0)
}
}
write.table(paste("<BR><BR><CENTER><TABLE border=0><TR>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
write.table("<TH BGCOLOR=\"#e0e0ff\"></TH>", file=paste(subPageClip, i,
".html", sep=""), append=T, quote=F, row.names=F, col.names=F)
for (j in stuff2[[3]][1]:stuff2[[3]][2]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Plate ", j, "</TH>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F, row.names=F,
col.names=F)
}
write.table("</TR>", file=paste(subPageClip, i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
write.table(paste("<TR><TH BGCOLOR=\"#e0e0ff\">Channel ", o, "</TH>",
sep=""), file=paste(subPageClip, i, ".html", sep=""), append=T,
quote=F, row.names=F, col.names=F)
for (j in stuff2[[3]][1]:stuff2[[3]][2]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", stuff2[[1]],
"_Exp_", i, "_PerPlate_", j, "_.pdf\"><IMG SRC=\"", stuff2[[1]], "_Exp_", i,
"_PerPlate_", j, "_.png\"/></A></CENTER><BR></TD>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
}
}
}
function4a<-function(header, dataset, vecOfChannels, posNegFlag, firstLineBis,
secondLineBis, indexOutput, subPage, flag){
##########
####4a####
##########
subPageClip1<-strsplit(subPage, ".html")
subPageClip<-subPageClip1[[1]][1]
subPageClip<-paste(subPageClip, "_", sep="")
if (posNegFlag == 1){
write.table("<BR><BR><BR><CENTER><H2>Distribution of controls</H2></CENTER>",
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><CENTER><TABLE border=0><TR>", file=indexOutput, append=T,
quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
write.table("<TR>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
for (i in 1:length(vecOfChannels)){
if (flag == 0){
zeugs<-controlDensity(header, dataset, vecOfChannels[i],
paste("Control density (", i, ")", sep=""), 0, 1)
}else{
zeugs<-controlDensity(header, dataset, vecOfChannels[i],
paste("norm. Control density (", flag, ") (", i, ")", sep=""), 0, 1)
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", subPage,
"\"><IMG SRC=\"", zeugs, ".png\"/></A></CENTER><BR></TD>", sep=""),
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=indexOutput, append=T, quote=F,
row.names=F, col.names=F)
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file=subPage, quote=F, row.names=F, col.names=F)
write.table("<CENTER><H2>Control density per experiment</H2></CENTER>",
file=subPage, append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><BR><CENTER><TABLE border=0><TR>", file=subPage,
append=T, quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subPage, append=T, quote=F, row.names=F,
col.names=F)
write.table("<TR>", file=subPage, append=T, quote=F, row.names=F,
col.names=F)
for (i in 1:length(vecOfChannels)){
if (flag == 0){
zeugs<-controlDensity(header, dataset, vecOfChannels[i],
paste("Control density (", i, ")", sep=""), 0, 1)
}else{
zeugs<-controlDensity(header, dataset, vecOfChannels[i],
paste("norm. Control density (", flag, ") (", i, ")", sep=""), 0, 1)
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", zeugs,
".pdf\"><IMG SRC=\"", zeugs, ".png\"/></A></CENTER><BR></TD>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=subPage, append=T, quote=F,
row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
if (flag == 0){
stuff<-controlDensityPerScreen(header, dataset, vecOfChannels[i],
paste("Control density (", i, ")", sep=""), 0, 1)
}else{
stuff<-controlDensityPerScreen(header, dataset, vecOfChannels[i],
paste("norm. Control density (", flag, ") (", i, ")", sep=""), 0, 1)
}
write.table(paste("<BR><BR><CENTER><TABLE border=0><TR>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
write.table("<TH BGCOLOR=\"#e0e0ff\"></TH>", file=subPage, append=T,
quote=F, row.names=F, col.names=F)
for (j in stuff[[2]]:stuff[[3]]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Exp. ", j, "</TH>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subPage, append=T, quote=F, row.names=F, col.names=F)
write.table(paste("<TR><TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
for (j in stuff[[2]]:stuff[[3]]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", subPageClip, j,
".html\"><IMG SRC=\"", stuff[[1]], "(Exp. ", j,
").png\"/></A></CENTER><BR></TD>", sep=""), file=subPage, append=T,
quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=subPage, append=T, quote=F,
row.names=F, col.names=F)
}
for (i in stuff[[2]]:stuff[[3]]){
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file=paste(subPageClip, i, ".html", sep=""),
quote=F, row.names=F, col.names=F)
write.table(paste("<CENTER><H2>Control density per plate for experiment ", i,
"</H2></CENTER>", sep=""), file=paste(subPageClip, i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><BR><CENTER><TABLE border=0><TR>", file=paste(subPageClip, i,
".html", sep=""), append=T, quote=F, row.names=F, col.names=F)
for (j in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", j, "</TH>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
}
write.table("</TR>", file=paste(subPageClip, i, ".html", sep=""), append=T,
quote=F, row.names=F, col.names=F)
write.table("<TR>", file=paste(subPageClip, i, ".html", sep=""), append=T,
quote=F, row.names=F, col.names=F)
for (j in 1:length(vecOfChannels)){
if (flag == 0){
zeugs<-controlDensityPerScreen(header, dataset, vecOfChannels[j],
paste("Control density (", j, ")", sep=""), 0, 1)
}else{
zeugs<-controlDensityPerScreen(header, dataset, vecOfChannels[j],
paste("norm. Control density (", flag, ") (", j, ")", sep=""), 0, 1)
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", zeugs[[1]],
"(Exp. ", i, ").pdf\"><IMG SRC=\"", zeugs[[1]], "(Exp. ", i,
").png\"/></A></CENTER><BR></TD>", sep=""), file=paste(subPageClip, i,
".html", sep=""), append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
for (o in 1:length(vecOfChannels)){
if (flag == 0){
stuff2<-controlDensityPerPlate(header, dataset, vecOfChannels[o],
paste("Control density (", o, ")", sep=""), 2, 0, 1)
}else{
stuff2<-controlDensityPerPlate(header, dataset, vecOfChannels[o],
paste("norm. Control density (, ", flag, ") (", o, ")", sep=""), 2, 0, 1)
}
write.table(paste("<BR><BR><CENTER><TABLE border=0><TR>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
write.table("<TH BGCOLOR=\"#e0e0ff\"></TH>",
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
for (j in stuff2[[3]][1]:stuff2[[3]][2]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Plate ", j, "</TH>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
}
write.table("</TR>", file=paste(subPageClip, i, ".html", sep=""), append=T,
quote=F, row.names=F, col.names=F)
write.table(paste("<TR><TH BGCOLOR=\"#e0e0ff\">Channel ", o, "</TH>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
for (j in stuff2[[3]][1]:stuff2[[3]][2]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", stuff2[[1]],
"_Exp_", i, "_PerPlate_", j, "_.pdf\"><IMG SRC=\"", stuff2[[1]], "_Exp_", i,
"_PerPlate_", j, "_.png\"/></A></CENTER><BR></TD>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
}
}
}
}
function4b<-function(header, dataset, vecOfChannels, posNegFlag, firstLineBis,
secondLineBis, indexOutput, subPage, flag){
##########
####4b####
##########
if (posNegFlag == 1){
write.table("<BR><BR><BR><CENTER><H2>Z' Factors</H2></CENTER>",
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><CENTER><TABLE border=0><TR>", file=indexOutput,
append=T, quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
write.table("<TR>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
for (i in 1:length(vecOfChannels)){
if (flag == 0){
zeugs<-ZPRIMEQualControl(header, dataset, vecOfChannels[i],
paste("Z' Factors (", i, ")", sep=""), 0)
}else{
zeugs<-ZPRIMEQualControl(header, dataset, vecOfChannels[i],
paste("Z' Factors (", flag, ") (", i, ") (norm.)", sep=""), 0)
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", subPage,
"\"><IMG SRC=\"", zeugs[[1]], ".png\"/></A></CENTER><BR></TD>", sep=""),
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=indexOutput, append=T, quote=F,
row.names=F, col.names=F)
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file=subPage, quote=F, row.names=F, col.names=F)
write.table("<CENTER><H2>Z' Factors</H2></CENTER>", file=subPage, append=T,
quote=F, row.names=F, col.names=F)
write.table("<BR><BR><CENTER><TABLE border=0><TR>", file=subPage, append=T,
quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""), file=subPage,
append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subPage, append=T, quote=F, row.names=F, col.names=F)
write.table("<TR>", file=subPage, append=T, quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
if (flag == 0){
zeugs<-ZPRIMEQualControl(header, dataset, vecOfChannels[i],
paste("Z' Factors (", i, ")", sep=""), 0)
}else{
zeugs<-ZPRIMEQualControl(header, dataset, vecOfChannels[i],
paste("Z' Factors (", flag, ") (", i, ") (norm.)", sep=""), 0)
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", zeugs[[1]],
".pdf\"><IMG SRC=\"", zeugs[[1]], ".png\"/></A></CENTER><BR></TD>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=subPage, append=T, quote=F,
row.names=F, col.names=F)
s1<-"<BR><BR><CENTER><TABLE border=0><TR><TH BGCOLOR=\"#d0d0f0\">"
s2<-"Exp. #</TH><TH BGCOLOR=\"#e0e0ff\">Plate #</TH>"
s3<-paste(s1, s2, sep="")
write.table(s3, file=subPage, append=T, quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#d0d0f0\">Z' Score Ch. ", i, "</TH>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subPage, append=T, quote=F, row.names=F, col.names=F)
for (i in 2:nrow(zeugs[[2]])){
write.table(paste("<TR><TD BGCOLOR=\"#e0e0f0\">", zeugs[[2]][i, 1],
"</TD><TD BGCOLOR=\"#f0f0ff\" align=center>", zeugs[[2]][i, 2], "</TD>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
for (j in 1:length(vecOfChannels)){
if (flag == 0){
zeugs<-ZPRIMEQualControl(header, dataset, vecOfChannels[j],
paste("Z' Factors (", j, ")", sep=""), 0)
}else{
zeugs<-ZPRIMEQualControl(header, dataset, vecOfChannels[j],
paste("Z' Factors (", flag, ") (", j, ") (norm.)", sep=""), 0)
}
write.table(paste("<TD BGCOLOR=\"#e0e0f0\" align=center>", zeugs[[2]][i, 3],
"</TD>", sep=""), file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subPage, append=T, quote=F, row.names=F,
col.names=F)
}
write.table("</TABLE></CENTER>", file=subPage, append=T, quote=F,
row.names=F, col.names=F)
}
}
function5<-function(header, dataset, vecOfChannels, posNegFlag, firstLineBis,
secondLineBis, indexOutput, subPage, flag){
#########
####5####
#########
subPageClip1<-strsplit(subPage, ".html")
subPageClip<-subPageClip1[[1]][1]
subPageClip<-paste(subPageClip, "_", sep="")
if (posNegFlag == 1){
write.table("<BR><BR><BR><CENTER><H2>Comparison of controls</H2></CENTER>",
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><CENTER><TABLE border=0><TR>", file=indexOutput, append=T,
quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
write.table("<TR>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
for (i in 1:length(vecOfChannels)){
if (flag == 0){
zeugs<-makeBoxplotControls(header, dataset, vecOfChannels[i],
paste("Comparison of controls (", i, ")", sep=""), 0)
}else{
zeugs<-makeBoxplotControls(header, dataset, vecOfChannels[i],
paste("Comparison of controls (", flag, ") (", i, ") (norm.)", sep=""), 0)
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", subPage,
"\"><IMG SRC=\"", zeugs, ".png\"/></A></CENTER><BR></TD>", sep=""),
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=indexOutput, append=T, quote=F,
row.names=F, col.names=F)
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file=subPage, quote=F, row.names=F, col.names=F)
write.table("<CENTER><H2>Comparison of controls per experiment<H2></CENTER>",
file=subPage, append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><BR><CENTER><TABLE border=0><TR>", file=subPage, append=T,
quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subPage, append=T, quote=F, row.names=F, col.names=F)
write.table("<TR>", file=subPage, append=T, quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
if (flag == 0){
zeugs<-makeBoxplotControls(header, dataset, vecOfChannels[i],
paste("Comparison of controls (", i, ")", sep=""), 0)
}else{
zeugs<-makeBoxplotControls(header, dataset, vecOfChannels[i],
paste("Comparison of controls (", flag, ") (", i, ") (norm.)", sep=""), 0)
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", zeugs,
".pdf\"><IMG SRC=\"", zeugs, ".png\"/></A></CENTER><BR></TD>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=subPage, append=T, quote=F,
row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
if (flag == 0){
stuff<-makeBoxplotControlsPerScreen(header, dataset, vecOfChannels[i],
paste("Comparison of controls (", i, ")", sep=""), 2, 0)
}else{
stuff<-makeBoxplotControlsPerScreen(header, dataset, vecOfChannels[i],
paste("Comparison of controls (", flag, ") (", i, ") (norm.)", sep=""), 2, 0)
}
write.table(paste("<BR><BR><CENTER><TABLE border=0><TR>", sep=""), file=subPage,
append=T, quote=F, row.names=F, col.names=F)
write.table("<TH BGCOLOR=\"#e0e0ff\"></TH>", file=subPage, append=T, quote=F,
row.names=F, col.names=F)
for (j in stuff[[2]]:stuff[[3]]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Exp. ", j, "</TH>", sep=""), file=subPage,
append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subPage, append=T, quote=F, row.names=F, col.names=F)
write.table(paste("<TR><TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
for (j in stuff[[2]]:stuff[[3]]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", subPageClip, j,
".html\"><IMG SRC=\"", stuff[[1]], " (Exp.", j,
").png\"/></A></CENTER><BR></TD>", sep=""), file=subPage, append=T, quote=F,
row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=subPage, append=T, quote=F,
row.names=F, col.names=F)
}
for (i in stuff[[2]]:stuff[[3]]){
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file=paste(subPageClip, i, ".html", sep=""),
quote=F, row.names=F, col.names=F)
s1<-"<CENTER><H2>Comparison of controls per plate for experiment "
s2<-"</H2></CENTER>"
write.table(paste(s1, i, s2, sep=""), file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><BR><CENTER><TABLE border=0><TR>", file=paste(subPageClip, i,
".html", sep=""), append=T, quote=F, row.names=F, col.names=F)
for (j in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", j, "</TH>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
}
write.table("</TR>", file=paste(subPageClip, i, ".html", sep=""), append=T,
quote=F, row.names=F, col.names=F)
write.table("<TR>", file=paste(subPageClip, i, ".html", sep=""), append=T,
quote=F, row.names=F, col.names=F)
for (j in 1:length(vecOfChannels)){
if (flag == 0){
zeugs<-makeBoxplotControlsPerScreen(header, dataset, vecOfChannels[j],
paste("Comparison of controls (", j, ")", sep=""), 2, 0)
}else{
zeugs<-makeBoxplotControlsPerScreen(header, dataset, vecOfChannels[j],
paste("Comparison of controls (", flag, ") (", j, ") (norm.)", sep=""), 2, 0)
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", zeugs[[1]],
" (Exp.", i, ").pdf\"><IMG SRC=\"", zeugs[[1]], " (Exp.", i,
").png\"/></A></CENTER><BR></TD>", sep=""), file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
for (o in 1:length(vecOfChannels)){
if (flag == 0){
stuff2<-makeBoxplotControlsPerPlate(header, dataset, vecOfChannels[o],
paste("Comparison of controls (", o, ")", sep=""), 2, 0)
}else{
stuff2<-makeBoxplotControlsPerPlate(header, dataset, vecOfChannels[o],
paste("Comparison of controls (", flag, ") (", o, ") (norm.)", sep=""), 2, 0)
}
write.table(paste("<BR><BR><CENTER><TABLE border=0><TR>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
write.table("<TH BGCOLOR=\"#e0e0ff\"></TH>", file=paste(subPageClip, i,
".html", sep=""), append=T, quote=F, row.names=F, col.names=F)
for (j in stuff2[[3]][1]:stuff2[[3]][2]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Plate ", j, "</TH>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
}
write.table("</TR>", file=paste(subPageClip, i, ".html", sep=""), append=T,
quote=F, row.names=F, col.names=F)
write.table(paste("<TR><TH BGCOLOR=\"#e0e0ff\">Channel ", o, "</TH>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
for (j in stuff2[[3]][1]:stuff2[[3]][2]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", stuff2[[1]],
"_Exp_", i, "_PerPlate", j, ".pdf\"><IMG SRC=\"", stuff2[[1]], "_Exp_", i,
"_PerPlate", j, ".png\"/></A></CENTER><BR></TD>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
}
}
}
}
function6<-function(header, dataset, vecOfChannels, firstLineBis,
secondLineBis, indexOutput, subPage, flag){
#########
####6####
#########
subPageClip1<-strsplit(subPage, ".html")
subPageClip<-subPageClip1[[1]][1]
subPageClip<-paste(subPageClip, "_", sep="")
write.table("<BR><BR><BR><CENTER><H2>QQ plots</H2></CENTER>", file=indexOutput,
append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><CENTER><TABLE border=0><TR>", file=indexOutput, append=T,
quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
write.table("<TR>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
for (i in 1:length(vecOfChannels)){
if (flag == 0){
zeugs<-plotQQ(header, dataset, vecOfChannels[i], paste("QQ plot (", i, ")",
sep=""), 0)
}else{
zeugs<-plotQQ(header, dataset, vecOfChannels[i], paste("QQ plot (", flag,
") (", i, ") (norm.)", sep=""), 0)
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", subPage,
"\"><IMG SRC=\"", zeugs, ".png\"/></A></CENTER><BR></TD>", sep=""),
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=indexOutput, append=T, quote=F,
row.names=F, col.names=F)
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file=subPage, quote=F, row.names=F, col.names=F)
write.table("<CENTER><H2>QQ plots per experiment</H2></CENTER>", file=subPage,
append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><BR><CENTER><TABLE border=0><TR>", file=subPage, append=T,
quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subPage, append=T, quote=F, row.names=F,
col.names=F)
write.table("<TR>", file=subPage, append=T, quote=F, row.names=F,
col.names=F)
for (i in 1:length(vecOfChannels)){
if (flag == 0){
zeugs<-plotQQ(header, dataset, vecOfChannels[i], paste("QQ plot (",
i, ")", sep=""), 0)
}else{
zeugs<-plotQQ(header, dataset, vecOfChannels[i], paste("QQ plot (",
flag, ") (", i, ") (norm.)", sep=""), 0)
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", zeugs,
".pdf\"><IMG SRC=\"", zeugs, ".png\"/></A></CENTER><BR></TD>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=subPage, append=T, quote=F,
row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
if (flag == 0){
stuff<-plotQQperscreen(header, dataset, vecOfChannels[i], paste("QQ plot (",
i, ")", sep=""), 2, 0)
}else{
stuff<-plotQQperscreen(header, dataset, vecOfChannels[i], paste("QQ plot (",
flag, ") (", i, ") (norm.)", sep=""), 2, 0)
}
write.table(paste("<BR><BR><CENTER><TABLE border=0><TR>", sep=""), file=subPage,
append=T, quote=F, row.names=F, col.names=F)
write.table("<TH BGCOLOR=\"#e0e0ff\"></TH>", file=subPage, append=T, quote=F,
row.names=F, col.names=F)
for (j in stuff[[2]]:stuff[[3]]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Exp. ", j, "</TH>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subPage, append=T, quote=F, row.names=F, col.names=F)
write.table(paste("<TR><TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
for (j in stuff[[2]]:stuff[[3]]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", subPageClip, j,
".html\"><IMG SRC=\"", stuff[[1]], " (Exp.", j,
").png\"/></A></CENTER><BR></TD>", sep=""), file=subPage, append=T, quote=F,
row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=subPage, append=T,
quote=F, row.names=F, col.names=F)
}
for (i in stuff[[2]]:stuff[[3]]){
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file=paste(subPageClip, i, ".html", sep=""),
quote=F, row.names=F, col.names=F)
s1<-"<CENTER><H2>Comparison of controls per plate for experiment "
s2<-"</H2></CENTER>"
write.table(paste(s1, i, s2, sep=""), file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><BR><CENTER><TABLE border=0><TR>", file=paste(subPageClip, i,
".html", sep=""), append=T, quote=F, row.names=F, col.names=F)
for (j in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", j, "</TH>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F, row.names=F,
col.names=F)
}
write.table("</TR>", file=paste(subPageClip, i, ".html", sep=""), append=T,
quote=F, row.names=F, col.names=F)
write.table("<TR>", file=paste(subPageClip, i, ".html", sep=""), append=T,
quote=F, row.names=F, col.names=F)
for (j in 1:length(vecOfChannels)){
if (flag == 0){
zeugs<-plotQQperscreen(header, dataset, vecOfChannels[j], paste("QQ plot (", j,
")", sep=""), 2, 0)
}else{
zeugs<-plotQQperscreen(header, dataset, vecOfChannels[j], paste("QQ plot (",
flag, ") (", j, ") (norm.)", sep=""), 2, 0)
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", zeugs[[1]],
" (Exp.", i, ").pdf\"><IMG SRC=\"", zeugs[[1]], " (Exp.", i,
").png\"/></A></CENTER><BR></TD>", sep=""), file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
for (o in 1:length(vecOfChannels)){
if (flag == 0){
stuff2<-plotQQperplate(header, dataset, vecOfChannels[o], paste("QQ plot (", o,
")", sep=""), 2, 0)
}else{
stuff2<-plotQQperplate(header, dataset, vecOfChannels[o], paste("QQ plot (",
flag, ") (", o, ") (norm.)", sep=""), 2, 0)
}
write.table(paste("<BR><BR><CENTER><TABLE border=0><TR>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
write.table("<TH BGCOLOR=\"#e0e0ff\"></TH>", file=paste(subPageClip, i,
".html", sep=""), append=T, quote=F, row.names=F, col.names=F)
for (j in stuff2[[3]][1]:stuff2[[3]][2]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Plate ", j, "</TH>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
}
write.table("</TR>", file=paste(subPageClip, i, ".html", sep=""), append=T,
quote=F, row.names=F, col.names=F)
write.table(paste("<TR><TH BGCOLOR=\"#e0e0ff\">Channel ", o, "</TH>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
for (j in stuff2[[3]][1]:stuff2[[3]][2]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", stuff2[[1]],
"Exp", i, "_PerPlate", j, ".pdf\"><IMG SRC=\"", stuff2[[1]], "Exp", i,
"_PerPlate", j, ".png\"/></A></CENTER><BR></TD>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
}
}
}
function7<-function(header, dataset, vecOfChannels, firstLineBis,
secondLineBis, indexOutput, subpageA, subpageB, flag, flagForNorm){
#########
####7####
#########
s1<-"<BR><BR><BR><CENTER><H2>Spearmans correlation coefficients</H2></CENTER>"
write.table(s1, file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><CENTER><TABLE border=0><TR>", file=indexOutput, append=T,
quote=F, row.names=F, col.names=F)
if (flag == 1){
for (j in 1:2){
for (i in 1:length(vecOfChannels)){
write.table(paste("<TH>Channel", i, "</TH>", sep=""), file=indexOutput,
append=T, quote=F, row.names=F, col.names=F)
}
}
}else{
for (i in 1:length(vecOfChannels)){
write.table(paste("<TH>Channel", i, "</TH>", sep=""), file=indexOutput,
append=T, quote=F, row.names=F, col.names=F)
}
}
write.table("</TR><TR>", file=indexOutput, append=T, quote=F,
row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
write.table("<TD>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
tableOfCoeffs<-replicatesSpearmancor(header, dataset, 1, vecOfChannels[i],
"GeneName", "per_experiment")
s2<-"<CENTER><TABLE border=0><TR><TH BGCOLOR=\"#d0d0f0\"></TH><TH BGCOLOR="
s3<-"\"#e0e0ff\">Rep. 1 vs. 2</TH><TH BGCOLOR=\"#d0d0f0\">Rep. 2 vs. 3</TH>"
s4<-"<TH BGCOLOR=\"#e0e0ff\">Rep. 1 vs. 3</TH></TR>"
s5<-paste(s2, s3, s4, sep="")
write.table(s5, file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
counter<-1
for (j in 1:max(tableOfCoeffs[, 1])){
write.table(paste("<TR><TD BGCOLOR=\"#e0e0f0\">Exp. ", j,
"</TD><TD BGCOLOR=\"#f0f0ff\" align=center>", tableOfCoeffs[counter, 4],
"</TD><TD BGCOLOR=\"#e0e0f0\" align=center>", tableOfCoeffs[(counter+1), 4],
"</TD><TD BGCOLOR=\"#f0f0ff\" align=center>", tableOfCoeffs[(counter+2), 4],
"</TD></TR>", sep=""), file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
counter<-counter+3
}
write.table("</CENTER></TABLE>", file=indexOutput, append=T, quote=F,
row.names=F, col.names=F)
write.table("</TD>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
}
if (flag == 1){
for (i in 1:length(vecOfChannels)){
write.table("<TD>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
tableOfCoeffs<-replicatesSpearmancor(header, dataset, 2, vecOfChannels[i],
"GeneName", "between_experiments")
s6<-"<CENTER><TABLE border=0><TR><TH BGCOLOR=\"#d0d0f0\">Exp.</TH><TH BGCOLOR="
s7<-"\"#e0e0ff\">Exp.</TH><TH BGCOLOR=\"#d0d0f0\">Correlation coeff.</TH></TR>"
s8<-paste(s6, s7, sep="")
write.table(s8, file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
for (j in 1:nrow(tableOfCoeffs)){
write.table(paste("<TR><TD BGCOLOR=\"#e0e0f0\">", tableOfCoeffs[j, 1],
"</TD><TD BGCOLOR=\"#f0f0ff\" align=center>", tableOfCoeffs[j, 2],
"</TD><TD BGCOLOR=\"#e0e0f0\" align=center>", tableOfCoeffs[j, 3],
"</TD></TR>", sep=""), file=indexOutput, append=T, quote=F,
row.names=F, col.names=F)
}
write.table("</CENTER></TABLE>", file=indexOutput, append=T, quote=F,
row.names=F, col.names=F)
write.table("</TD>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
}
}
write.table("</TR></CENTER></TABLE>", file=indexOutput, append=T, quote=F,
row.names=F, col.names=F)
s9<-"<A HREF=\""
s1<-"\">Correlation of variation plots</A>, <A HREF=\""
s2<-"\">Plots for replicate comparison</A>"
write.table(paste(s9, subpageA, s1, subpageB, s2, sep=""), file=indexOutput,
append=T, quote=F, row.names=F, col.names=F)
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file=subpageA, quote=F, row.names=F, col.names=F)
write.table("<CENTER><H2>Correlation of variation</H2></CENTER>", file=subpageA,
append=T, quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
stuff<-replicatesCV(header, dataset, paste("Correlation of variation (",
flagForNorm, ") (", i, ")", sep=""), vecOfChannels[i], "GeneName", 2, 0)
write.table(paste("<BR><BR><CENTER><TABLE border=0><TR>", sep=""),
file=subpageA, append=T, quote=F, row.names=F, col.names=F)
write.table("<TH BGCOLOR=\"#e0e0ff\"></TH>", file=subpageA, append=T, quote=F,
row.names=F, col.names=F)
for (j in stuff[[2]]:stuff[[3]]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Exp. ", j, "</TH>", sep=""),
file=subpageA, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subpageA, append=T, quote=F, row.names=F, col.names=F)
write.table(paste("<TR><TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=subpageA, append=T, quote=F, row.names=F, col.names=F)
for (j in stuff[[2]]:stuff[[3]]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", stuff[[1]],
" (Exp.", j, ").pdf\"><IMG SRC=\"", stuff[[1]], " (Exp.", j,
").png\"/></A></CENTER><BR></TD>", sep=""), file=subpageA, append=T,
quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=subpageA, append=T, quote=F,
row.names=F, col.names=F)
}
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file=subpageB, quote=F, row.names=F, col.names=F)
write.table("<CENTER><H2>Comparison of replicates</H2></CENTER>",
file=subpageB, append=T, quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
if (i>1){
write.table("<BR>", file=subpageB, append=T, quote=F, row.names=F, col.names=F)
}
write.table(paste("<BR><CENTER>Channel ", i, "</CENTER>", sep=""),
file=subpageB, append=T, quote=F, row.names=F, col.names=F)
stuff<-compareReplicates(header, dataset, paste("Comparison of replicates (",
flagForNorm, ") (", i, ")", sep=""), vecOfChannels[i], "GeneName", 2, 0)
for (j in stuff[[2]]:stuff[[3]]){
write.table(paste("<CENTER><TABLE border=0><TR><TH BGCOLOR=\"#e0e0ff\">Exp.",
j, "</TH>", sep=""), file=subpageB, append=T, quote=F, row.names=F, col.names=F)
for (k in 1:stuff[[4]]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", stuff[[1]],
"_Exp_", j, "(", k, ").pdf\"><IMG SRC=\"", stuff[[1]], "_Exp_", j, "(", k,
").png\"/></A></CENTER><BR></TD>", sep=""), file=subpageB, append=T, quote=F,
row.names=F, col.names=F)
}
}
write.table("</TR></CENTER></TABLE>", file=subpageB, append=T, quote=F,
row.names=F, col.names=F)
}
}
vennDiagfunc<-function(hitVectors, hitVectorsTestNames, hitScoringVec1,
listOfArgs4stat){
typeOfScoringVec<-rep(NA_character_, length(hitVectors))
typeOfComparison<-rep(NA_character_, length(hitVectors))
saveif<-0
if (hitScoringVec1[1] == 1){
for (i in 1:length(hitVectorsTestNames)){
if (hitVectorsTestNames[[i]] == "t test"
| hitVectorsTestNames[[i]] == "Mann-Whitney test"){
if (listOfArgs4stat[[i]][1] == "l"){
typeOfScoringVec[i]<-"l"
typeOfComparison[i]<-"P"
}
if (listOfArgs4stat[[i]][1] == "g"){
typeOfScoringVec[i]<-"g"
typeOfComparison[i]<-"P"
}
if (listOfArgs4stat[[i]][1] == "two.sided"){
typeOfScoringVec[i]<-"two.sided"
typeOfComparison[i]<-"P"
}
}
if (hitVectorsTestNames[[i]] == "Rank product test"){
if (listOfArgs4stat[[i]][2] == 1){
typeOfScoringVec[i]<-"l"
typeOfComparison[i]<-"P"
}else{
typeOfScoringVec[i]<-"g"
typeOfComparison[i]<-"P"
}
}
}
}
if (hitScoringVec1[2] == 1 | hitScoringVec1[2] == 2){
saveif<-length(which(typeOfScoringVec == "l"))
for (g in 1:saveif){
if(sum(is.na(typeOfScoringVec))!=0){
##if there are NAs in typeOfScoringVec
ind<-min(which(is.na(typeOfScoringVec)))
typeOfScoringVec[ind]<-"l"
if (hitScoringVec1[2] == 1){
typeOfComparison[ind]<-"Z"
}
if (hitScoringVec1[2] == 2){
typeOfComparison[ind]<-"PZ"
}
}
}
}
if (hitScoringVec1[3] == 1 | hitScoringVec1[3] == 2){
saveif<-length(which(typeOfScoringVec == "g"))
for (g in 1:saveif){
if(sum(is.na(typeOfScoringVec))!=0){
##if there are NAs in typeOfScoringVec
ind<-min(which(is.na(typeOfScoringVec)))
typeOfScoringVec[ind]<-"g"
if (hitScoringVec1[3] == 1){
typeOfComparison[ind]<-"Z"
}
if (hitScoringVec1[3] == 2){
typeOfComparison[ind]<-"PZ"
}
}
}
}
invisible(list(typeOfScoringVec, typeOfComparison))
}
listChooseIndex<-function(fullList, chooseVec){
for (g in 1:length(chooseVec)){
if (g == 1){
partList<-list(fullList[[chooseVec[g]]])
}else{
partList[[g]]<-fullList[[chooseVec[g]]]
}
}
invisible(partList)
}
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Defines functions listChooseIndex vennDiagfunc function7 function6 function5 function4b function4a function3 function2 function1 gseaTableFunc mainAnalysis
Documented in mainAnalysis
mainAnalysis <- function(header, dataset, flagForSameExp, listOfNormalizations,
listOfArgs4norm, listOfStatTests, listOfArgs4stat, multTestAdj, hitScoringVec1,
hitScoringVec2, posNegFlag, flag4Gsea, vecOfChannels, whichOnto){
warning("The mainAnalysis() routine is deprecated. Please use rnaither() instead.")
firstLine<-strsplit(header[[1]], ",")
firstLineBis<-firstLine[[1]][2]
secondLine<-strsplit(header[[2]], ",")
secondLineBis<-secondLine[[1]][2]
thirdLine<-strsplit(header[[3]], "comments,")
thirdLineBis<-thirdLine[[1]][2]
#################################
##########QUALITY PLOTS##########
#################################
print(paste("Computing quality plots on raw data...", date(), sep=": "))
##MAINPAGE titles:
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file="index.html", quote=F, row.names=F, col.names=F)
write.table(paste("<BODY><CENTER><H1>", firstLineBis, "</H1></CENTER>", sep=""),
file="index.html", append=T, quote=F, row.names=F, col.names=F)
##SUBPAGE1 titles:
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file="sub1.html", quote=F, row.names=F, col.names=F)
write.table(paste("<BODY><CENTER><H2>Boxplots per Plate</H2></CENTER>", sep=""),
file="sub1.html", append=T, quote=F, row.names=F, col.names=F)
print(paste("Generating boxplots of signals...", date(), sep=": "))
function1(header, dataset, vecOfChannels, firstLineBis, secondLineBis,
"index.html", "sub1.html", 0)
print(paste("Generating spatial distribution of signals...", date(), sep=": "))
function2(header, dataset, vecOfChannels, firstLineBis, secondLineBis,
"index.html", "sub2.html", 0)
print(paste("Plotting signals per well...", date(), sep=": "))
function2b(header, dataset, vecOfChannels, firstLineBis, secondLineBis,
"index.html", "sub2b.html", 0)
if (length(vecOfChannels)>1){
print(paste("Comparing channels...", date(), sep=": "))
function2c(header, dataset, vecOfChannels, firstLineBis, secondLineBis,
"index.html", "sub2c.html", 0)
}
print(paste("Plotting histogram distribution of signals...", date(), sep=": "))
function3(header, dataset, vecOfChannels, posNegFlag, firstLineBis,
secondLineBis, "index.html", "sub3.html", 0)
print(paste("Plotting control densities...", date(), sep=": "))
function4a(header, dataset, vecOfChannels, posNegFlag, firstLineBis,
secondLineBis, "index.html", "sub4a.html", 0)
print(paste("Computing Z'factors...", date(), sep=": "))
function4b(header, dataset, vecOfChannels, posNegFlag, firstLineBis,
secondLineBis, "index.html", "sub4b.html", 0)
print(paste("Generating boxplots of control signals...", date(), sep=": "))
function5(header, dataset, vecOfChannels, posNegFlag, firstLineBis,
secondLineBis, "index.html", "sub5.html", 0)
print(paste("Generating QQ plots...", date(), sep=": "))
function6(header, dataset, vecOfChannels, firstLineBis, secondLineBis,
"index.html", "sub6.html", 0)
write.table("</BODY>", file="index.html", append=T, quote=F, row.names=F,
col.names=F)
write.table("</BODY>", file="sub1.html", append=T, quote=F, row.names=F,
col.names=F)
write.table("</BODY>", file="sub2.html", append=T, quote=F, row.names=F,
col.names=F)
write.table("</BODY>", file="sub2b.html", append=T, quote=F, row.names=F,
col.names=F)
write.table("</BODY>", file="sub2c.html", append=T, quote=F, row.names=F,
col.names=F)
write.table("</BODY>", file="sub3.html", append=T, quote=F, row.names=F,
col.names=F)
write.table("</BODY>", file="sub4a.html", append=T, quote=F, row.names=F,
col.names=F)
write.table("</BODY>", file="sub4b.html", append=T, quote=F, row.names=F,
col.names=F)
write.table("</BODY>", file="sub5.html", append=T, quote=F, row.names=F,
col.names=F)
write.table("</BODY>", file="sub6.html", append=T, quote=F, row.names=F,
col.names=F)
################################
##########NORMALIZATION#########
################################
print(paste("Normalizing data...", date(), sep=": "))
for (i in 1:length(listOfNormalizations)){
result<-listOfNormalizations[[i]](header, dataset, listOfArgs4norm[[i]])
header<-result[[1]]
dataset<-result[[2]]
##change Inf and -Inf values that potentially arise during normalization to NA
##it is IMPORTANT for this that the argument order for normalization functions stays the same!
col4plot<-listOfArgs4norm[[i]][[1]][1]
if(length(which(dataset[[get("col4plot")]]==Inf))>0){
places<-which(dataset[[get("col4plot")]]==Inf)
dataset[[get("col4plot")]][places]=NA
}
if(length(which(dataset[[get("col4plot")]]==-Inf))>0){
places<-which(dataset[[get("col4plot")]]==-Inf)
dataset[[get("col4plot")]][places]=NA
}
saveDataset(header, dataset, paste(firstLineBis, "_Fulldataset.txt", sep=""))
#################################
##########QUALITY PLOTS##########
#################################
print("Computing quality plots on normalized data...")
thirdLine<-strsplit(header[[3]], "comments,")
thirdLineBis<-thirdLine[[1]][2]
##MAINPAGE titles:
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file=paste("indexnorm", i, ".html", sep=""),
quote=F, row.names=F, col.names=F)
write.table(paste("<BODY><CENTER><H1>", firstLineBis, " after normalization",
"</H1></CENTER>", sep=""), file=paste("indexnorm", i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
write.table(paste("<CENTER>(", thirdLineBis, ")</CENTER>", sep=""),
file=paste("indexnorm", i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
##SUBPAGE1 titles:
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file=paste("sub1norm", i, ".html", sep=""),
quote=F, row.names=F, col.names=F)
write.table(paste("<BODY><CENTER><H1>Boxplots per Plate</H1></CENTER>", sep=""),
file=paste("sub1norm", i, ".html", sep=""), append=T, quote=F, row.names=F,
col.names=F)
print(paste("Generating boxplots of signals...", date(), sep=": "))
function1(header, dataset, vecOfChannels, firstLineBis, secondLineBis,
paste("indexnorm", i, ".html", sep=""), paste("sub1norm", i, ".html", sep=""),
i)
print(paste("Generating spatial distribution of signals...", date(), sep=": "))
function2(header, dataset, vecOfChannels, firstLineBis, secondLineBis,
paste("indexnorm", i, ".html", sep=""), paste("sub2norm", i, ".html", sep=""),
i)
print(paste("Plotting signals per well...", date(), sep=": "))
function2b(header, dataset, vecOfChannels, firstLineBis, secondLineBis,
paste("indexnorm", i, ".html", sep=""), paste("sub2bnorm", i, ".html", sep=""),
i)
if (length(vecOfChannels)>1){
print(paste("Comparing channels...", date(), sep=": "))
function2c(header, dataset, vecOfChannels, firstLineBis, secondLineBis,
paste("indexnorm", i, ".html", sep=""), paste("sub2cnorm", i, ".html", sep=""),
i)
}
print(paste("Plotting histogram distribution of signals...", date(), sep=": "))
function3(header, dataset, vecOfChannels, posNegFlag, firstLineBis,
secondLineBis, paste("indexnorm", i, ".html", sep=""),
paste("sub3norm", i, ".html", sep=""), i)
print(paste("Plotting control densities...", date(), sep=": "))
function4a(header, dataset, vecOfChannels, posNegFlag, firstLineBis,
secondLineBis, paste("indexnorm", i, ".html", sep=""),
paste("sub4anorm", i, ".html", sep=""), i)
print(paste("Computing Z'factors...", date(), sep=": "))
function4b(header, dataset, vecOfChannels, posNegFlag, firstLineBis,
secondLineBis, paste("indexnorm", i, ".html", sep=""),
paste("sub4bnorm", i, ".html", sep=""), i)
print(paste("Generating boxplots of control signals...", date(), sep=": "))
function5(header, dataset, vecOfChannels, posNegFlag, firstLineBis,
secondLineBis, paste("indexnorm", i, ".html", sep=""),
paste("sub5norm", i, ".html", sep=""), i)
print(paste("Generating QQ plots...", date(), sep=": "))
function6(header, dataset, vecOfChannels, firstLineBis, secondLineBis,
paste("indexnorm", i, ".html", sep=""), paste("sub6norm", i, ".html", sep=""),
i)
print(paste("Computing Spearman's correlation coefficients...", date(),
sep=": "))
function7(header, dataset, vecOfChannels, firstLineBis, secondLineBis,
paste("indexnorm", i, ".html", sep=""), paste("sub7anorm", i, ".html", sep=""),
paste("sub7bnorm", i, ".html", sep=""), flagForSameExp, i)
write.table("</BODY>", file=paste("indexnorm", i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
write.table("</BODY>", file=paste("sub1norm", i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
write.table("</BODY>", file=paste("sub2norm", i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
write.table("</BODY>", file=paste("sub2bnorm", i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
write.table("</BODY>", file=paste("sub2cnorm", i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
write.table("</BODY>", file=paste("sub3norm", i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
write.table("</BODY>", file=paste("sub4anorm", i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
write.table("</BODY>", file=paste("sub4bnorm", i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
write.table("</BODY>", file=paste("sub5norm", i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
write.table("</BODY>", file=paste("sub6norm", i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
write.table("</BODY>", file=paste("sub7anorm", i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
write.table("</BODY>", file=paste("sub7bnorm", i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
}
##############################
##########STAT TESTS##########
##############################
print(paste("Performing statistical tests...", date(), sep=": "))
##MAINPAGE titles:
write.table(paste("<HTML><HEAD><TITLE>Statistical analysis report, ",
secondLineBis, ", ", firstLineBis, "</TITLE></HEAD>", sep=""),
file="stats.html", quote=F, row.names=F, col.names=F)
##MAINPAGE Seitentitel:
write.table(paste("<BODY><CENTER><H1>Statistical analysis report, ",
firstLineBis, "</H1></CENTER>", sep=""), file="stats.html", append=T,
quote=F, row.names=F, col.names=F)
write.table(paste("<CENTER>(Normalizations performed: ", thirdLineBis,
")</CENTER>", sep=""), file="stats.html", append=T, quote=F,
row.names=F, col.names=F)
##Apply statistical tests and score hits:
hitVectors<-list("platzhalter")
hitVectorsTestNames<-list("platzhalter")
counterHitVectorsTestnames<-0
for (i in 1:length(listOfStatTests)){
testResult<-listOfStatTests[[i]](dataset, listOfArgs4stat[[i]])
pValVec<-testResult[[1]]
dataset<-testResult[[2]]
namepValVec<-testResult[[3]]
saveDataset(header, dataset, paste(firstLineBis, "_Fulldataset.txt", sep=""))
##adjust for multiple testing and reinsert pValVec into dataset:
pValVec<-multTestAdjust(pValVec, multTestAdj)
temp<-generateReplicateMat(dataset, 1, "Intensities", listOfArgs4stat[[i]][[3]],
listOfArgs4stat[[i]][[4]])
dataset<-incorporatepValVec(dataset, pValVec, temp[[1]],
listOfArgs4stat[[i]][[4]], paste(namepValVec, "_adjusted_", multTestAdj,
sep=""))
print(paste("Scoring hits...", date(), sep=": "))
result<-hitselectionPval(dataset, pValVec, listOfArgs4stat[[i]][[3]],
paste("hits_", namepValVec, "_adjusted_", multTestAdj, sep=""),
hitScoringVec2[1], listOfArgs4stat[[i]][[4]], paste("pval_hits_",
testResult[[4]], " (", i, ").txt", sep=""))
dataset<-result[[1]]
hitVectors[[i]]<-result[[2]]
hitVectorsTestNames[[i]]<-testResult[[4]]
hitThreshold<-round(result[[4]], digits=2)
if (hitScoringVec1[1] == 1){
##scoring according to only p-value
genesnPvals<-read.table(paste("pval_hits_", testResult[[4]], " (", i,
").txt", sep=""))
if (hitVectorsTestNames[[i]] == "Mann-Whitney test"
| hitVectorsTestNames[[i]] == "t test"){
if (listOfArgs4stat[[i]][[1]] == "g"){
upOrDownReg<-"Upregulated"
}
if (listOfArgs4stat[[i]][[1]] == "l"){
upOrDownReg<-"Downregulated"
}
if (listOfArgs4stat[[i]][[1]] == "two.sided"){
upOrDownReg<-"Up and downregulated"
}
}
if (hitVectorsTestNames[[i]] == "Rank product test"){
if (listOfArgs4stat[[i]][[2]] == 1){
upOrDownReg<-"Downregulated"
}
if (listOfArgs4stat[[i]][[2]] == 2){
upOrDownReg<-"Upregulated"
}
}
write.table(paste("<br><br><br><CENTER><H2>", upOrDownReg,
" genes according to ", hitVectorsTestNames[[i]],
"</H2> (multiple testing adjument: ", multTestAdj, ") (p-value < ",
hitThreshold, ") - <a href=\"", "pval_hits_", testResult[[4]], " (", i, ").txt",
"\">Textfile</a> -</CENTER>", sep=""), file="stats.html", append=T, quote=F,
row.names=F, col.names=F)
s1<-"<CENTER><TABLE border=0><TR><TH BGCOLOR=\"#d0d0f0\">Gene name</TH>"
s2<-"<TH BGCOLOR=\"#e0e0ff\">p-value</TH><TH BGCOLOR=\"#d0d0f0\">Median</TH>"
s3<-paste(s1, s2, sep="")
write.table(s3, file="stats.html", append=T, quote=F, row.names=F, col.names=F)
for (m in 1:(ncol(genesnPvals)-2)){
write.table("<TH BGCOLOR=\"#d0d0f0\">Norm val</TH>", file="stats.html",
append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
for (n in 1:nrow(genesnPvals)){
write.table(paste("<TR><TD BGCOLOR=\"#e0e0f0\">", rownames(genesnPvals)[n],
"</TD>", sep=""), file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
for (p in 1:ncol(genesnPvals)){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\" align=center>", genesnPvals[n, p],
"</TD>", sep=""), file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
}
write.table("</TR>", file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
}
write.table("</CENTER></TABLE>", file="stats.html", append=T, quote=F,
row.names=F, col.names=F)
##VOLCANO PLOT###
volcPlotName<-volcanoPlot(header, dataset, listOfArgs4stat[[i]][[3]],
paste(namepValVec, "_adjusted_", multTestAdj, sep=""),
listOfArgs4stat[[i]][[4]], paste("Volcano plot (", i, ")_p", sep=""),
hitScoringVec2[1], 0)
write.table("<br><br><CENTER>Volcano plot</CENTER><br>", file="stats.html",
append=T, quote=F, row.names=F, col.names=F)
write.table(paste("<CENTER><A HREF=\"", volcPlotName, ".pdf\"><IMG SRC=\"",
volcPlotName, ".png\"/></A></CENTER>", sep=""), file="stats.html", append=T,
quote=F, row.names=F, col.names=F)
##SPATIAL DISTRIBUTION OF HITS
res<-spatialDistribHits(header, dataset, paste("Spatial hits distribution (",
i, ")_p", sep=""), paste("hits_", namepValVec, "_adjusted_", multTestAdj,
sep=""), listOfArgs4stat[[i]][[4]], 0)
write.table("<BR><BR><CENTER><TABLE border=0><TR><TH BGCOLOR=\"#e0e0ff\"></TH>",
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
for (j in res[[3]][1]:res[[3]][2]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Plate ", j, "</TH>", sep=""),
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file="stats.html", append=T, quote=F, row.names=F, col.names=F)
for (k in res[[2]][1]:res[[2]][2]){
write.table(paste("<TR><TH BGCOLOR=\"#e0e0ff\">Exp. ", k, "</TH>", sep=""),
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
for (m in res[[3]][1]:res[[3]][2]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", res[[1]],
"_Exp_", k, "_Plate_", m, "_.html", "\"><IMG SRC=\"", res[[1]], "_Exp_", k,
"_Plate_", m, "_4html.png\"/></A></CENTER><BR></TD>", sep=""),
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
}
}
write.table("</TR></CENTER></TABLE>", file="stats.html", append=T, quote=F,
row.names=F, col.names=F)
}
if (hitScoringVec1[2] == 2 ){
##hitscoring according to zSc < thresh & pval < thresh in hitScoringVec2[1]
if (((hitVectorsTestNames[[i]] == "Mann-Whitney test"
| hitVectorsTestNames[[i]] == "t test")
& (listOfArgs4stat[[i]][[1]] == "two.sided"
| listOfArgs4stat[[i]][[1]] == "l"))
| (hitVectorsTestNames[[i]] == "Rank product test"
& listOfArgs4stat[[i]][[2]] == 1)){
result<-hitselectionZscorePval(dataset, pValVec, listOfArgs4stat[[i]][[3]],
paste("hits_", namepValVec, "_adjusted_", multTestAdj, "_ZScore<",
hitScoringVec2[2], sep=""), hitScoringVec2[2], hitScoringVec2[1], -2,
listOfArgs4stat[[i]][[4]], median, paste("pval_hits_", testResult[[4]],
"combined_ZSc_sm_", hitScoringVec2[2], ".txt", sep=""))
dataset<-result[[1]]
counterHitVectorsTestnames<-counterHitVectorsTestnames+1
hitVectors[[length(listOfStatTests)+counterHitVectorsTestnames]]<-result[[2]]
hitThresholdZsc<-round(result[[3]], digits=3)
hitThresholdPval<-round(result[[4]], digits=2)
s3<-paste(testResult[[4]], " & ZScore sm ", hitThresholdZsc, sep="")
hitVectorsTestNames[[length(listOfStatTests)+counterHitVectorsTestnames]]<-s3
genesnPvals<-read.table(paste("pval_hits_", testResult[[4]], "combined_ZSc_sm_",
hitScoringVec2[2], ".txt", sep=""))
upOrDownReg<-"Downregulated"
write.table(paste("<br><br><br><CENTER><H2>", upOrDownReg,
" genes according to ", hitVectorsTestNames[[length(listOfStatTests)
+counterHitVectorsTestnames]], "</H2> (multiple testing adjument: ",
multTestAdj, ") (Thresholds: pval < ", hitThresholdPval, ", Z-score < ",
hitThresholdZsc, ") - <a href=\"", "pval_hits_", testResult[[4]],
"combined_ZSc_sm_", hitScoringVec2[2], ".txt", "\">Textfile</a> -</CENTER>",
sep=""), file="stats.html", append=T, quote=F, row.names=F, col.names=F)
s5<-"<CENTER><TABLE border=0><TR><TH BGCOLOR=\"#d0d0f0\">Gene name</TH>"
s6<-"<TH BGCOLOR=\"#e0e0ff\">sumZScore</TH><TH BGCOLOR=\"#e0e0ff\">p-value</TH>"
s7<-paste(s5, s6, sep="")
write.table(s7, file="stats.html", append=T, quote=F, row.names=F, col.names=F)
for (m in 1:(ncol(genesnPvals)-2)){
write.table("<TH BGCOLOR=\"#d0d0f0\">Norm val</TH>", file="stats.html",
append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
for (n in 1:nrow(genesnPvals)){
write.table(paste("<TR><TD BGCOLOR=\"#e0e0f0\">", rownames(genesnPvals)[n],
"</TD>", sep=""), file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
for (p in 1:ncol(genesnPvals)){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\" align=center>",
genesnPvals[n, p], "</TD>", sep=""), file="stats.html", append=T,
quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
}
write.table("</CENTER></TABLE>", file="stats.html", append=T,
quote=F, row.names=F, col.names=F)
##VOLCANO PLOT###
if (hitScoringVec1[3] == 2){
volcPlotName<-volcanoPlot(header, dataset, listOfArgs4stat[[i]][[3]],
paste(namepValVec, "_adjusted_", multTestAdj, sep=""),
listOfArgs4stat[[i]][[4]], paste("Volcano plot (", i, ")_zl", sep=""),
c(hitScoringVec2[1], hitScoringVec2[2], hitScoringVec2[3]), 0)
}else{
volcPlotName<-volcanoPlot(header, dataset, listOfArgs4stat[[i]][[3]],
paste(namepValVec, "_adjusted_", multTestAdj, sep=""),
listOfArgs4stat[[i]][[4]], paste("Volcano plot (", i, ")_zl", sep=""),
c(hitScoringVec2[1], hitScoringVec2[2]), 0)
}
write.table("<br><br><CENTER>Volcano plot</CENTER><br>", file="stats.html",
append=T, quote=F, row.names=F, col.names=F)
write.table(paste("<CENTER><A HREF=\"", volcPlotName, ".pdf\"><IMG SRC=\"",
volcPlotName, ".png\"/></A></CENTER>", sep=""), file="stats.html",
append=T, quote=F, row.names=F, col.names=F)
res<-spatialDistribHits(header, dataset, paste("Spatial hits distribution (",
i, ")_zl", sep=""), paste("hits_", namepValVec, "_adjusted_", multTestAdj,
"_ZScore<", hitScoringVec2[2], sep=""), listOfArgs4stat[[i]][[4]], 0)
write.table("<BR><BR><CENTER><TABLE border=0><TR><TH BGCOLOR=\"#e0e0ff\"></TH>",
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
for (j in res[[3]][1]:res[[3]][2]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Plate ", j, "</TH>", sep=""),
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
for (k in res[[2]][1]:res[[2]][2]){
write.table(paste("<TR><TH BGCOLOR=\"#e0e0ff\">Exp. ", k, "</TH>", sep=""),
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
for (m in res[[3]][1]:res[[3]][2]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", res[[1]],
"_Exp_", k, "_Plate_", m, "_.html", "\"><IMG SRC=\"", res[[1]], "_Exp_", k,
"_Plate_", m, "_4html.png\"/></A></CENTER><BR></TD>", sep=""),
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
}
}
write.table("</TR></CENTER></TABLE>", file="stats.html", append=T,
quote=F, row.names=F, col.names=F)
}
}
if (hitScoringVec1[3] == 2){
##hitscoring according to zSc > thresh & pval < thresh in hitScoringVec2[1]
if (((hitVectorsTestNames[[i]] == "Mann-Whitney test"
| hitVectorsTestNames[[i]] == "t test")
& (listOfArgs4stat[[i]][[1]] == "two.sided"
| listOfArgs4stat[[i]][[1]] == "g"))
| (hitVectorsTestNames[[i]] == "Rank product test"
& listOfArgs4stat[[i]][[2]] == 2)){
result<-hitselectionZscorePval(dataset, pValVec, listOfArgs4stat[[i]][[3]],
paste("hits_", namepValVec, "_adjusted_", multTestAdj, "_ZScore>",
hitScoringVec2[3], sep=""), hitScoringVec2[3], hitScoringVec2[1], 2,
listOfArgs4stat[[i]][[4]], median, paste("pval_hits_", testResult[[4]],
"combined_ZSc_gr_", hitScoringVec2[3], ".txt", sep=""))
dataset<-result[[1]]
counterHitVectorsTestnames<-counterHitVectorsTestnames+1
hitVectors[[length(listOfStatTests)+counterHitVectorsTestnames]]<-result[[2]]
hitThresholdZsc<-round(result[[3]], digits=3)
hitThresholdPval<-round(result[[4]], digits=2)
hitVectorsTestNames[[length(listOfStatTests)+counterHitVectorsTestnames]]<-
paste(testResult[[4]], " & ZScore gr ", hitThresholdZsc, sep="")
genesnPvals<-read.table(paste("pval_hits_", testResult[[4]], "combined_ZSc_gr_",
hitScoringVec2[3], ".txt", sep=""))
upOrDownReg<-"Upregulated"
write.table(paste("<br><br><br><CENTER><H2>", upOrDownReg,
" genes according to ", hitVectorsTestNames[[length(listOfStatTests)
+counterHitVectorsTestnames]], "</H2> (multiple testing adjument: ",
multTestAdj, ") (Thresholds: p-value < ", hitThresholdPval, ", Z-score > ",
hitThresholdZsc, ") - <a href=\"", "pval_hits_", testResult[[4]],
"combined_ZSc_gr_", hitScoringVec2[3], ".txt", "\">Textfile</a> -</CENTER>",
sep=""), file="stats.html", append=T, quote=F, row.names=F, col.names=F)
s8<-"<CENTER><TABLE border=0><TR><TH BGCOLOR=\"#d0d0f0\">Gene name</TH>"
s9<-"<TH BGCOLOR=\"#e0e0ff\">sumZScore</TH><TH BGCOLOR=\"#e0e0ff\">p-value</TH>"
s1<-paste(s8, s9, sep="")
write.table(s1, file="stats.html", append=T, quote=F, row.names=F, col.names=F)
for (m in 1:(ncol(genesnPvals)-2)){
write.table("<TH BGCOLOR=\"#d0d0f0\">Norm val</TH>", file="stats.html",
append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
for (n in 1:nrow(genesnPvals)){
write.table(paste("<TR><TD BGCOLOR=\"#e0e0f0\">", rownames(genesnPvals)[n],
"</TD>", sep=""), file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
for (p in 1:ncol(genesnPvals)){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\" align=center>", genesnPvals[n, p],
"</TD>", sep=""), file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
}
write.table("</TR>", file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
}
write.table("</CENTER></TABLE>", file="stats.html", append=T, quote=F,
row.names=F, col.names=F)
##VOLCANO PLOT###
if (hitScoringVec1[3] == 2){
volcPlotName<-volcanoPlot(header, dataset, listOfArgs4stat[[i]][[3]],
paste(namepValVec, "_adjusted_", multTestAdj, sep=""),
listOfArgs4stat[[i]][[4]], paste("Volcano plot (", i, ")_zg", sep=""),
c(hitScoringVec2[1], hitScoringVec2[2], hitScoringVec2[3]), 0)
}else{
volcPlotName<-volcanoPlot(header, dataset, listOfArgs4stat[[i]][[3]],
paste(namepValVec, "_adjusted_", multTestAdj, sep=""),
listOfArgs4stat[[i]][[4]], paste("Volcano plot (", i, ")_zg", sep=""),
c(hitScoringVec2[1], hitScoringVec2[2]), 0)
}
write.table("<br><br><CENTER>Volcano plot</CENTER><br>", file="stats.html",
append=T, quote=F, row.names=F, col.names=F)
write.table(paste("<CENTER><A HREF=\"", volcPlotName, ".pdf\"><IMG SRC=\"",
volcPlotName, ".png\"/></A></CENTER>", sep=""), file="stats.html", append=T,
quote=F, row.names=F, col.names=F)
res<-spatialDistribHits(header, dataset, paste("Spatial hits distribution (",
i, ")_zg", sep=""), paste("hits_", namepValVec, "_adjusted_", multTestAdj,
"_ZScore>", hitScoringVec2[3], sep=""), listOfArgs4stat[[i]][[4]], 0)
write.table("<BR><BR><CENTER><TABLE border=0><TR><TH BGCOLOR=\"#e0e0ff\"></TH>",
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
for (j in res[[3]][1]:res[[3]][2]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Plate ", j, "</TH>", sep=""),
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
for (k in res[[2]][1]:res[[2]][2]){
write.table(paste("<TR><TH BGCOLOR=\"#e0e0ff\">Exp. ", k, "</TH>", sep=""),
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
for (m in res[[3]][1]:res[[3]][2]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", res[[1]],
"_Exp_", k, "_Plate_", m, "_.html", "\"><IMG SRC=\"", res[[1]], "_Exp_", k,
"_Plate_", m, "_4html.png\"/></A></CENTER><BR></TD>", sep=""),
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
}
}
write.table("</TR></CENTER></TABLE>", file="stats.html", append=T,
quote=F, row.names=F, col.names=F)
}
}
}
if (hitScoringVec1[2] == 1){
##scoring according to ZScore with ZScore <= threshold
result<-hitselectionZscore(dataset, "SigIntensity", "hits_ZScore_do",
hitScoringVec2[2], 2, -2, "GeneName", median, "ZScore_hits_smallerthresh.txt")
dataset<-result[[1]]
count<-length(hitVectors)
hitVectors[[count+1]]<-result[[2]]
hitVectorsTestNames[[count+1]]<-"ZScore_do"
hitThreshold<-round(result[[3]], digits=3)
res<-spatialDistribHits(header, dataset, "Spatial hits distribution (ZScore)",
"hits_ZScore_do", "GeneName", 0)
genesnPvals<-read.table("ZScore_hits_smallerthresh.txt")
write.table(paste("<br><br><br><CENTER><H2>Downregulated genes according to ",
hitVectorsTestNames[[count+1]], "</H2> (Threshold: Z-score < ", hitThreshold,
") - <a href=\"ZScore_hits_smallerthresh.txt\">Textfile</a> -</CENTER>",
sep=""), file="stats.html", append=T, quote=F, row.names=F, col.names=F)
s2<-"<CENTER><TABLE border=0><TR><TH BGCOLOR=\"#d0d0f0\">Gene name</TH>"
s3<-"<TH BGCOLOR=\"#e0e0ff\">ZScore (median)</TH>"
s4<-paste(s2, s3, sep="")
write.table(s4, file="stats.html", append=T, quote=F, row.names=F, col.names=F)
for (m in 1:(ncol(genesnPvals)-1)){
write.table("<TH BGCOLOR=\"#d0d0f0\">Norm val</TH>", file="stats.html",
append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
for (n in 1:nrow(genesnPvals)){
write.table(paste("<TR><TD BGCOLOR=\"#e0e0f0\">", rownames(genesnPvals)[n],
"</TD>", sep=""), file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
for (p in 1:ncol(genesnPvals)){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\" align=center>", genesnPvals[n, p],
"</TD>", sep=""), file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
}
write.table("</TR>", file="stats.html", append=T, quote=F,
row.names=F, col.names=F)
}
write.table("</CENTER></TABLE>", file="stats.html", append=T, quote=F,
row.names=F, col.names=F)
##SPATIAL DISTRIBUTION OF HITS - output
write.table("<BR><BR><CENTER><TABLE border=0><TR><TH BGCOLOR=\"#e0e0ff\"></TH>",
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
for (j in res[[3]][1]:res[[3]][2]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Plate ", j, "</TH>", sep=""),
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
for (k in res[[2]][1]:res[[2]][2]){
write.table(paste("<TR><TH BGCOLOR=\"#e0e0ff\">Exp. ", k, "</TH>", sep=""),
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
for (m in res[[3]][1]:res[[3]][2]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", res[[1]],
"_Exp_", k, "_Plate_", m, "_.html", "\"><IMG SRC=\"", res[[1]], "_Exp_", k,
"_Plate_", m, "_4html.png\"/></A></CENTER><BR></TD>", sep=""),
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
}
}
write.table("</TR></CENTER></TABLE>", file="stats.html", append=T, quote=F,
row.names=F, col.names=F)
}
if (hitScoringVec1[3] == 1){
result<-hitselectionZscore(dataset, "SigIntensity", "hits_ZScore_up",
hitScoringVec2[3], 2, 2, "GeneName", median, "ZScore_hits_higherthresh.txt")
dataset<-result[[1]]
count<-length(hitVectors)
hitVectors[[count+1]]<-result[[2]]
hitVectorsTestNames[[count+1]]<-"ZScore_up"
hitThreshold<-round(result[[3]], digits=3)
res<-spatialDistribHits(header, dataset, "Spatial hits distribution (ZScore)",
"hits_ZScore_up", "GeneName", 0)
genesnPvals<-read.table("ZScore_hits_higherthresh.txt")
write.table(paste("<br><br><br><CENTER><H2>Upregulated genes according to ",
hitVectorsTestNames[[count+1]], "</H2> (Threshold: Z-score >", hitThreshold,
") - <a href=\"ZScore_hits_higherthresh.txt\">Textfile</a> -</CENTER>", sep=""),
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
s6<-"<CENTER><TABLE border=0><TR><TH BGCOLOR=\"#d0d0f0\">Gene name</TH>"
s7<-"<TH BGCOLOR=\"#e0e0ff\">ZScore (median)</TH>"
s8<-paste(s6, s7, sep="")
write.table(s8, file="stats.html", append=T, quote=F, row.names=F, col.names=F)
for (m in 1:(ncol(genesnPvals)-1)){
write.table("<TH BGCOLOR=\"#d0d0f0\">Norm val</TH>", file="stats.html",
append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
for (n in 1:nrow(genesnPvals)){
write.table(paste("<TR><TD BGCOLOR=\"#e0e0f0\">", rownames(genesnPvals)[n],
"</TD>", sep=""), file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
for (p in 1:ncol(genesnPvals)){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\" align=center>", genesnPvals[n, p],
"</TD>", sep=""), file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
}
write.table("</TR>", file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
}
write.table("</CENTER></TABLE>", file="stats.html", append=T, quote=F,
row.names=F, col.names=F)
##SPATIAL DISTRIBUTION OF HITS - output
write.table("<BR><BR><CENTER><TABLE border=0><TR><TH BGCOLOR=\"#e0e0ff\"></TH>",
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
for (j in res[[3]][1]:res[[3]][2]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Plate ", j, "</TH>", sep=""),
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
for (k in res[[2]][1]:res[[2]][2]){
write.table(paste("<TR><TH BGCOLOR=\"#e0e0ff\">Exp. ", k, "</TH>", sep=""),
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
for (m in res[[3]][1]:res[[3]][2]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", res[[1]],
"_Exp_", k, "_Plate_", m, "_.html", "\"><IMG SRC=\"", res[[1]], "_Exp_", k,
"_Plate_", m, "_4html.png\"/></A></CENTER><BR></TD>", sep=""),
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
}
}
write.table("</TR></CENTER></TABLE>", file="stats.html", append=T, quote=F,
row.names=F, col.names=F)
}
blob<-vennDiagfunc(hitVectors, hitVectorsTestNames, hitScoringVec1,
listOfArgs4stat)
typeOfScoringVec<-blob[[1]]
typeOfComparison<-blob[[2]]
write.table("<br><br><br><CENTER><H2>Venn diagrams:</H2></CENTER><br>",
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><CENTER><TABLE border=0><TR>", file="stats.html", append=T,
quote=F, row.names=F, col.names=F)
for (element in c("l", "g", "two.sided")){
if (length(which(typeOfScoringVec == element))>1){
if (element == "l"){
write.table("<TH BGCOLOR=\"#e0e0ff\">Downregulated genes</TH>",
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
}
if (element == "g"){
write.table("<TH BGCOLOR=\"#e0e0ff\">Upregulated genes</TH>",
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
}
if (element == "two.sided"){
write.table("<TH BGCOLOR=\"#e0e0ff\">Up- and downregulated genes</TH>",
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
}
}
}
write.table("</TR><TR>", file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
##make the venn diagram plots:
for (element in c("l", "g", "two.sided")){
if (length(which(typeOfScoringVec == element))>1){
write.table("<TD BGCOLOR=\"#f0f0ff\"><CENTER><TABLE border=0><TR>",
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
for (compType in c("P", "Z", "PZ")){
if (length(which(typeOfComparison == compType
& typeOfScoringVec == element))>1){
arg4venn2<-as.list(hitVectorsTestNames[which(typeOfComparison == compType
& typeOfScoringVec == element)])
chosenScoringVecIndexes<-which((typeOfScoringVec == element)
& (typeOfComparison == compType))
arg4venn1<-listChooseIndex(hitVectors, chosenScoringVecIndexes)
if (length(arg4venn1) == 2 | length(arg4venn1) == 3){
vennPlotName<-vennDiag(header, arg4venn1, arg4venn2,
paste("Venn Diagram (", element, ") (", compType, ")", sep=""), 0)
write.table(paste("<TH><A HREF=\"", vennPlotName, ".pdf\"><IMG SRC=\"",
vennPlotName, ".png\"/></A></TH>", sep=""), file="stats.html", append=T,
quote=F, row.names=F, col.names=F)
}
}
}
write.table("</TD></TR></CENTER></TABLE>", file="stats.html", append=T,
quote=F, row.names=F, col.names=F)
}
}
write.table("</TR></CENTER></TABLE>", file="stats.html", append=T,
quote=F, row.names=F, col.names=F)
##LINK TO FULL DATASET:
saveDataset(header, dataset, paste(firstLineBis, "_Fulldataset.txt", sep=""))
write.table(paste("<br><br><br><CENTER><a href=\"", firstLineBis,
"_Fulldataset.txt\">Full scored dataset</a></CENTER><br>", sep=""),
file="stats.html", append=T, quote=F, row.names=F, col.names=F)
##GSEA analysis
if(length(flag4Gsea)==1){
if(flag4Gsea==1){
print(paste("Performing GSEA analysis...", date(), sep=": "))
GOlist<-gseaAnalysisPt1(hitVectors[[1]], whichOnto)
for (g in 1:length(hitVectors)){
if (sum(hitVectors[[g]])>2 & sum(hitVectors[[g]])<length(hitVectors[[g]])){
geneTable<-gseaAnalysisPt2(hitVectors[[g]], GOlist, whichOnto)
write.table(geneTable, file=paste(firstLineBis, "_GSEAanalysis_",
hitVectorsTestNames[[g]], " (", typeOfScoringVec[[g]], ").txt", sep=""))
gseaTab<-read.table(paste(firstLineBis, "_GSEAanalysis_",
hitVectorsTestNames[[g]], " (", typeOfScoringVec[[g]], ").txt", sep=""))
gseaTableFunc(gseaTab, paste(firstLineBis, "_GSEAanalysis_",
hitVectorsTestNames[[g]], " (", typeOfScoringVec[[g]], ").txt", sep=""),
paste("Results of GSEA analysis for ", hitVectorsTestNames[[g]], " (",
typeOfScoringVec[[g]], ")", sep=""), paste("subGSEA", g, ".html", sep=""))
write.table(paste("<br><CENTER><a href=\"subGSEA", g,
".html\">Results of GSEA analysis for ", hitVectorsTestNames[[g]], " (",
typeOfScoringVec[[g]], ")</a></CENTER>", sep=""), file="stats.html",
append=T, quote=F, row.names=F, col.names=F)
}
}
}
}else{
print(paste("Performing GSEA analysis...", date(), sep=": "))
GOlist<-gseaAnalysisPt1(hitVectors[[1]], whichOnto)
for(i in 1:length(listOfStatTests)){
for (j in 1:length(hitScoringVec1)){
if(hitScoringVec1[j]>0){
indexNum<-(3-length(which(hitScoringVec1==0)))
g<-(j+(i-1)*indexNum)
if (flag4Gsea[g]==1 & sum(hitVectors[[g]])>2 & sum(hitVectors[[g]])<length(hitVectors[[g]])){
geneTable<-gseaAnalysisPt2(hitVectors[[g]], GOlist, whichOnto)
write.table(geneTable, file=paste(firstLineBis, "_GSEAanalysis_",
hitVectorsTestNames[[g]], " (", typeOfScoringVec[[g]], ").txt", sep=""))
gseaTab<-read.table(paste(firstLineBis, "_GSEAanalysis_",
hitVectorsTestNames[[g]], " (", typeOfScoringVec[[g]], ").txt", sep=""))
gseaTableFunc(gseaTab, paste(firstLineBis, "_GSEAanalysis_",
hitVectorsTestNames[[g]], " (", typeOfScoringVec[[g]], ").txt", sep=""),
paste("Results of GSEA analysis for ", hitVectorsTestNames[[g]], " (",
typeOfScoringVec[[g]], ")", sep=""), paste("subGSEA", g, ".html", sep=""))
write.table(paste("<br><CENTER><a href=\"subGSEA", g,
".html\">Results of GSEA analysis for ", hitVectorsTestNames[[g]], " (",
typeOfScoringVec[[g]], ")</a></CENTER>", sep=""), file="stats.html",
append=T, quote=F, row.names=F, col.names=F)
}
}
}
}
}
write.table("</BODY>", file="stats.html", append=T, quote=F, row.names=F,
col.names=F)
s1<-"Analysis finished. Quality analysis of raw data can be found in index.html"
s2<-", quality analysis of normalized data can be found in indexnorm.html. "
s3<-"Statistical analysis can be found in stats.html. "
s4<-date()
print(paste(s1, s2, s3, s4, sep=""))
}
gseaTableFunc<-function(gseaTab, gseaTabfile, gseaTitle, nameOfHtmlPage){
write.table(paste("<BR><BR><CENTER><H2>", gseaTitle, "</H2><a href=\"",
gseaTabfile, "\">Textfile</a></CENTER><br><br><CENTER><TABLE border=0><TR>",
sep=""), file=nameOfHtmlPage, quote=F, row.names=F, col.names=F)
for (i in 1:length(colnames(gseaTab))){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">", colnames(gseaTab)[i], "</TH>",
sep=""), file=nameOfHtmlPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=nameOfHtmlPage, append=T, quote=F, row.names=F,
col.names=F)
for (j in 1:nrow(gseaTab)){
write.table("<TR>", file=nameOfHtmlPage, append=T, quote=F, row.names=F,
col.names=F)
for (k in 1:ncol(gseaTab)){
write.table(paste("<TD BGCOLOR=\"#e0e0f0\">", gseaTab[j, k], "</TD>", sep=""),
file=nameOfHtmlPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=nameOfHtmlPage, append=T, quote=F, row.names=F,
col.names=F)
}
write.table("</TABLE></CENTER>", file=nameOfHtmlPage, append=T, quote=F,
row.names=F, col.names=F)
}
function1<-function(header, dataset, vecOfChannels, firstLineBis, secondLineBis, indexOutput, subPage, flag){
#########
####1####
#########
write.table("<BR><BR><CENTER><TABLE border=0><TR>", file=subPage, append=T,
quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subPage, append=T, quote=F, row.names=F,
col.names=F)
write.table("<TR>", file=subPage, append=T, quote=F, row.names=F,
col.names=F)
for (i in 1:length(vecOfChannels)){
if (flag == 0){
namePlot1<-makeBoxplotPerScreen(header, dataset, vecOfChannels[i],
paste("Data (", i, ") per Exp.", sep=""), 0)
}else{
namePlot1<-makeBoxplotPerScreen(header, dataset, vecOfChannels[i],
paste("norm. Data (", flag, ") (", i, ") per Exp.", sep=""), 0)
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"",
namePlot1, ".pdf\"><IMG SRC=\"", namePlot1, ".png\"/></A></CENTER><BR></TD>",
sep=""), file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subPage, append=T, quote=F, row.names=F,
col.names=F)
for (i in 1:length(vecOfChannels)){
if (flag == 0){
stuff<-makeBoxplotPerPlate(header, dataset, vecOfChannels[i],
paste("Data (", i, ") per Plate", sep=""), 2, 0)
}else{
stuff<-makeBoxplotPerPlate(header, dataset, vecOfChannels[i],
paste("norm. Data (", flag, ") (", i, ") per Plate", sep=""), 2, 0)
}
s1<-"<BR><BR><CENTER><TABLE border=0><TR><TD BGCOLOR=\"#e0e0f0\"><H3 align="
s2<-"left>Channel"
s3<-"</H3></TD>"
write.table(paste(s1, s2, i, s3, sep=""), file=subPage, append=T,
quote=F, row.names=F, col.names=F)
for (j in stuff[[2]]:stuff[[3]]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"",
stuff[[1]], "(Exp. ", j, ").pdf\"><IMG SRC=\"", stuff[[1]], "(Exp. ", j,
").png\"/></A></CENTER><BR></TD>", sep=""), file=subPage, append=T,
quote=F, row.names=F, col.names=F)
}
}
for (i in 1:length(vecOfChannels)){
if (flag == 0){
stuff<-makeBoxplot4PlateType(header, dataset, vecOfChannels[i],
paste("Data (", i, ") per Exp.", sep=""), 0)
}else{
stuff<-makeBoxplot4PlateType(header, dataset, vecOfChannels[i],
paste("norm. Data (", flag, ") (", i, ") per Exp.", sep=""), 0)
}
s4<-"<BR><BR><CENTER><TABLE border=0><TR><TD BGCOLOR=\"#e0e0f0\"><H3 align=left"
s5<-">Channel"
s6<-"</H3></TD>"
write.table(paste(s4, s5, i, s6, sep=""), file=subPage, append=T, quote=F,
row.names=F, col.names=F)
for (j in stuff[[2]]:stuff[[3]]){ #for each plate type / for each plot
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"",
stuff[[1]], " for Plate", j, ".pdf\"><IMG SRC=\"", stuff[[1]],
" for Plate", j, ".png\"/></A></CENTER><BR></TD>", sep=""), file=subPage,
append=T, quote=F, row.names=F, col.names=F)
}
}
write.table("<BR><BR><CENTER><TABLE border=0><TR>", file=indexOutput,
append=T, quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
write.table("<TR>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
for (i in 1:length(vecOfChannels)){
if (flag == 0){
namePlot1<-makeBoxplotPerScreen(header, dataset, vecOfChannels[i],
paste("Data (", i, ") per Exp.", sep=""), 0)
}else{
namePlot1<-makeBoxplotPerScreen(header, dataset, vecOfChannels[i],
paste("norm. Data (", flag, ") (", i, ") per Exp.", sep=""), 0)
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", subPage,
"\"><IMG SRC=\"", namePlot1, ".png\"/></A></CENTER><BR></TD>", sep=""),
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=indexOutput, append=T,
quote=F, row.names=F, col.names=F)
}
function2<-function(header, dataset, vecOfChannels, firstLineBis,
secondLineBis, indexOutput, subPage, flag){
#########
####2####
#########
s1<-"<br><br><br><CENTER><H2>Spatial distribution of Intensities</H2></CENTER>"
write.table(s1, file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
if (flag == 0){
stuff2<-spatialDistrib(header, dataset, paste("Spatial I distribution (", i,
")", sep=""), vecOfChannels[i], "Internal_GeneID", 0)
}else{
stuff2<-spatialDistrib(header, dataset, paste("norm. Spatial I distribution (",
flag, ") (", i, ")", sep=""), vecOfChannels[i], "Internal_GeneID", 0)
}
if (i>1){
write.table("<BR>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
}
s2<-"<BR><CENTER><TABLE border=0><TR><TH BGCOLOR=\"#e0e0ff\">Channel "
write.table(paste(s2, i, "</TH>", sep=""), file=indexOutput, append=T,
quote=F, row.names=F, col.names=F)
for (j in stuff2[[3]][1]:stuff2[[3]][2]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Plate ", j, "</TH>", sep=""),
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
for (k in stuff2[[2]][1]:stuff2[[2]][2]){
write.table(paste("<TR><TH BGCOLOR=\"#e0e0ff\">Exp. ", k, "</TH>", sep=""),
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
for (m in stuff2[[3]][1]:stuff2[[3]][2]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", stuff2[[1]],
"_Exp_", k, "_Plate_", m, "_.html", "\"><IMG SRC=\"", stuff2[[1]], "_Exp_", k,
"_Plate_", m, "_4html.png\"/></A></CENTER><BR></TD>", sep=""), file=indexOutput,
append=T, quote=F, row.names=F, col.names=F)
}
}
write.table("</TR></CENTER></TABLE>", file=indexOutput, append=T, quote=F,
row.names=F, col.names=F)
}
s4<-"<br><br><br><CENTER><H2>Standard deviation of Intensities</H2></CENTER>"
write.table(s4, file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><CENTER><TABLE border=0><TR>", file=indexOutput, append=T,
quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=indexOutput, append=T, quote=F,
row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
if (flag == 0){
zeugs<-compareReplicateSD(header, dataset, paste("SD (", i, ") of replicates",
sep=""), vecOfChannels[i], "GeneName", 0)
}else{
zeugs<-compareReplicateSD(header, dataset, paste("SD (", i,
") of norm. replicates (", flag, ")", sep=""), vecOfChannels[i], "GeneName", 0)
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", subPage,
"\"><IMG SRC=\"", zeugs, " 4html.png\"/></A></CENTER><BR></TD>", sep=""),
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=indexOutput, append=T, quote=F,
row.names=F, col.names=F)
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file=subPage, quote=F, row.names=F, col.names=F)
s1<-"<CENTER><H2>Standard deviation of Intensities per experiment</H2></CENTER>"
write.table(s1, file=subPage, append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><BR><CENTER><TABLE border=0><TR>", file=subPage, append=T,
quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subPage, append=T, quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
if (flag == 0){
zeugs<-compareReplicateSD(header, dataset, paste("SD (", i, ") of replicates",
sep=""), vecOfChannels[i], "GeneName", 0)
}else{
zeugs<-compareReplicateSD(header, dataset, paste("SD (", i,
") of norm. replicates (", flag, ")", sep=""), vecOfChannels[i], "GeneName", 0)
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", zeugs,
" .html\"><IMG SRC=\"", zeugs, " 4html.png\"/></A></CENTER><BR></TD>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=subPage, append=T, quote=F,
row.names=F, col.names=F)
write.table(paste("<BR><BR><CENTER><TABLE border=0><TR>", sep=""), file=subPage,
append=T, quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
write.table("<TH BGCOLOR=\"#e0e0ff\"></TH>", file=subPage, append=T,
quote=F, row.names=F, col.names=F)
if (flag == 0){
stuff<-compareReplicateSDPerScreen(header, dataset, paste("SD (", i,
") of replicates", sep=""), vecOfChannels[i], "GeneName", 0)
}else{
stuff<-compareReplicateSDPerScreen(header, dataset, paste("SD (", i,
") of norm. replicates (", flag, ")", sep=""), vecOfChannels[i], "GeneName", 0)
}
for (j in stuff[[2]]:stuff[[3]]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Exp. ", j, "</TH>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subPage, append=T, quote=F, row.names=F, col.names=F)
write.table(paste("<TR><TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
for (j in stuff[[2]]:stuff[[3]]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", stuff[[1]],
"_Exp_", j, "_.html\"><IMG SRC=\"", stuff[[1]], "_Exp_", j,
"_4html.png\"/></A></CENTER><BR></TD>", sep=""), file=subPage, append=T,
quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</CENTER></TABLE>", file=subPage, append=T, quote=F,
row.names=F, col.names=F)
}
function2b <-function (header, dataset, vecOfChannels,
firstLineBis, secondLineBis, indexOutput, subPage, flag){
##########
####2b####
##########
subPageClip1<-strsplit(subPage, ".html")
subPageClip<-subPageClip1[[1]][1]
subPageClip<-paste(subPageClip, "_", sep="")
s1<-"<BR><BR><BR><CENTER><H2>Distribution of data per well</H2></CENTER>"
write.table(s1, sep="", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
numOfScreens<-max(dataset$ScreenNb)
minOfScreens<-min(dataset$ScreenNb)
write.table(paste("<BR><BR><CENTER>", sep=""), file=indexOutput,
append=T, quote=F, row.names=F, col.names=F)
for (i in minOfScreens:numOfScreens){
write.table(paste("<A HREF=\"", subPageClip, i, ".html\">Experiment ",
i, "</A><br>", sep=""), file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file=paste(subPageClip, i, ".html", sep=""),
quote=F, row.names=F, col.names=F)
for (o in 1:length(vecOfChannels)){
if (flag == 0){
stuff2<-ZScorePlotTwo(header, dataset, 2, 1, vecOfChannels[o],
"GeneName", paste("Data per well (", o, ")", sep=""), 0)
}else{
stuff2<-ZScorePlotTwo(header, dataset, 2, 1, vecOfChannels[o], "GeneName",
paste("norm. Data per well (", flag, ") (", o, ")", sep=""), 0)
}
write.table(paste("<BR><BR><CENTER><TABLE border=0><TR>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
write.table("<TH BGCOLOR=\"#e0e0ff\"></TH>", file=paste(subPageClip, i,
".html", sep=""), append=T, quote=F, row.names=F, col.names=F)
for (j in stuff2[[3]][1]:stuff2[[3]][2]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Plate ", j, "</TH>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
}
write.table("</TR>", file=paste(subPageClip, i, ".html", sep=""), append=T,
quote=F, row.names=F, col.names=F)
write.table(paste("<TR><TH BGCOLOR=\"#e0e0ff\">Channel ", o, "</TH>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F, row.names=F,
col.names=F)
for (j in stuff2[[3]][1]:stuff2[[3]][2]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", stuff2[[1]],
"_Exp_", i, "_Plate_", j, "_.pdf\"><IMG SRC=\"", stuff2[[1]], "_Exp_", i,
"_Plate_", j, "_.png\"/></A></CENTER><BR></TD>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
}
}
write.table(paste("</CENTER>", sep=""), file=indexOutput, append=T, quote=F,
row.names=F, col.names=F)
}
function2c <-function (header, dataset, vecOfChannels, firstLineBis,
secondLineBis, indexOutput, subPage, flag){
##########
####2c####
##########
subPageClip1<-strsplit(subPage, ".html")
subPageClip<-subPageClip1[[1]][1]
subPageClip<-paste(subPageClip, "_", sep="")
combinationNum<-choose(length(vecOfChannels), 2)
write.table("<BR><BR><BR><CENTER><H2>Comparison of channels</H2></CENTER>",
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><CENTER><TABLE border=0><TR>", file=indexOutput, append=T,
quote=F, row.names=F, col.names=F)
if (flag == 0){
zeugs<-channelPlot(header, dataset, vecOfChannels, 0, "Channel comparison", 0)
}else{
zeugs<-channelPlot(header, dataset, vecOfChannels, 0,
paste("Channel comparison (", flag, ")", sep=""), 0)
}
for (i in 1:length(combinationNum)){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", subPage,
"\"><IMG SRC=\"", zeugs, "(", i, ").png\"/></A></CENTER><BR></TD>", sep=""),
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=indexOutput, append=T, quote=F,
row.names=F, col.names=F)
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file=subPage, quote=F, row.names=F, col.names=F)
write.table("<CENTER><H2>Comparison of channels - per experiment</H2></CENTER>",
file=subPage, append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><BR><CENTER><TABLE border=0><TR>", file=subPage, append=T,
quote=F, row.names=F, col.names=F)
if (flag == 0){
zeugs<-channelPlot(header, dataset, vecOfChannels, 0, "Channel comparison", 0)
}else{
zeugs<-channelPlot(header, dataset, vecOfChannels, 0,
paste("Channel comparison (", flag, ")", sep=""), 0)
}
for (i in 1:length(combinationNum)){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", zeugs, "(", i,
").pdf\"><IMG SRC=\"", zeugs, "(", i, ").png\"/></A></CENTER><BR></TD>",
sep=""), file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=subPage, append=T, quote=F,
row.names=F, col.names=F)
if (flag == 0){
stuff<-channelPlot(header, dataset, vecOfChannels, 1, "Channel comparison", 0)
}else{
stuff<-channelPlot(header, dataset, vecOfChannels, 1,
paste("Channel comparison (", flag, ")", sep=""), 0)
}
write.table(paste("<BR><BR><CENTER><TABLE border=0><TR>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
for (j in stuff[[2]]:stuff[[3]]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Exp. ", j, "</TH>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subPage, append=T, quote=F, row.names=F,
col.names=F)
for (i in 1:length(combinationNum)){
write.table(paste("<TR>", sep=""), file=subPage, append=T, quote=F,
row.names=F, col.names=F)
for (j in stuff[[2]]:stuff[[3]]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", subPageClip, j,
".html\"><IMG SRC=\"", stuff[[1]], "(", i, ") (Exp. ", j,
").png\"/></A></CENTER><BR></TD>", sep=""), file=subPage, append=T, quote=F,
row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=subPage, append=T, quote=F,
row.names=F, col.names=F)
}
for (i in stuff[[2]]:stuff[[3]]){
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file=paste(subPageClip, i, ".html", sep=""),
quote=F, row.names=F, col.names=F)
s1<-"<CENTER><H2>Comparison of channels - per plate for experiment "
s2<-"</H2></CENTER>"
write.table(paste(s1, i, s2, sep=""), file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><BR><CENTER><TABLE border=0><TR>", file=paste(subPageClip, i,
".html", sep=""), append=T, quote=F, row.names=F, col.names=F)
if (flag == 0){
zeugs<-channelPlot(header, dataset, vecOfChannels, 1, "Channel comparison", 0)
}else{
zeugs<-channelPlot(header, dataset, vecOfChannels, 1,
paste("Channel comparison (", flag, ")", sep=""), 0)
}
for (j in 1:length(combinationNum)){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", zeugs[[1]], "(",
j, ") (Exp. ", i, ").pdf\"><IMG SRC=\"", zeugs[[1]], "(", j, ") (Exp. ", i,
").png\"/></A></CENTER><BR></TD>", sep=""), file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
if (flag == 0){
stuff2<-channelPlot(header, dataset, vecOfChannels, 2, "Channel comparison", 0)
}else{
stuff2<-channelPlot(header, dataset, vecOfChannels, 2,
paste("Channel comparison (", flag, ")", sep=""), 0)
}
write.table(paste("<BR><BR><CENTER><TABLE border=0><TR>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
for (j in stuff2[[3]][1]:stuff2[[3]][2]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Plate", j, "</TH>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
}
write.table(paste("</TR>", sep=""), file=paste(subPageClip, i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
for (o in 1:length(combinationNum)){
write.table(paste("<TR>", sep=""), file=paste(subPageClip, i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
for (j in stuff2[[3]][1]:stuff2[[3]][2]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", stuff2[[1]],
"(", o, ")_Exp_", i, "_Plate_", j, "_.pdf\"><IMG SRC=\"", stuff2[[1]], "(", o,
")_Exp_", i, "_Plate_", j, "_.png\"/></A></CENTER><BR></TD>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F, row.names=F,
col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
}
}
}
function3<-function(header, dataset, vecOfChannels, posNegFlag, firstLineBis,
secondLineBis, indexOutput, subPage, flag){
#########
####3####
#########
subPageClip1<-strsplit(subPage, ".html")
subPageClip<-subPageClip1[[1]][1]
subPageClip<-paste(subPageClip, "_", sep="")
write.table("<BR><BR><BR><CENTER><H2>Distribution of data</H2></CENTER>",
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><CENTER><TABLE border=0><TR>", file=indexOutput, append=T,
quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
write.table("<TR>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
for (i in 1:length(vecOfChannels)){
if (posNegFlag == 0){
if (flag == 0){
zeugs<-plotHisto(header, dataset, vecOfChannels[i],
paste("Distribution of Data (", i, ")", sep=""), 0)
}else{
zeugs<-plotHisto(header, dataset, vecOfChannels[i],
paste("Distribution of norm. Data (", flag, ") (", i, ")", sep=""), 0)
}
}else{
if (flag == 0){
zeugs<-plotControlHisto(header, dataset, vecOfChannels[i],
paste("Distribution of Data and Controls (", i, ")", sep=""), 0)
}else{
zeugs<-plotControlHisto(header, dataset, vecOfChannels[i],
paste("Distribution of norm. Data (", flag, ") and Controls (", i, ")",
sep=""), 0)
}
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", subPage,
"\"><IMG SRC=\"", zeugs, ".png\"/></A></CENTER><BR></TD>", sep=""),
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=indexOutput, append=T,
quote=F, row.names=F, col.names=F)
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file=subPage, quote=F, row.names=F, col.names=F)
write.table("<CENTER><H2>Distribution of data per experiment</H2></CENTER>",
file=subPage, append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><BR><CENTER><TABLE border=0><TR>", file=subPage, append=T,
quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subPage, append=T, quote=F, row.names=F, col.names=F)
write.table("<TR>", file=subPage, append=T, quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
if (posNegFlag == 0){
if (flag == 0){
zeugs<-plotHisto(header, dataset, vecOfChannels[i],
paste("Distribution of Data (", i, ")", sep=""), 0)
}else{
zeugs<-plotHisto(header, dataset, vecOfChannels[i],
paste("Distribution of norm. Data (", flag, ") (", i, ")", sep=""), 0)
}
}else{
if (flag == 0){
zeugs<-plotControlHisto(header, dataset, vecOfChannels[i],
paste("Distribution of Data and Controls (", i, ")", sep=""), 0)
}else{
zeugs<-plotControlHisto(header, dataset, vecOfChannels[i],
paste("Distribution of norm. Data (", flag, ") and Controls (", i,
")", sep=""), 0)
}
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", zeugs,
".pdf\"><IMG SRC=\"", zeugs, ".png\"/></A></CENTER><BR></TD>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=subPage, append=T, quote=F,
row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
if (posNegFlag == 0){
if (flag == 0){
stuff<-plotHistoPerscreen(header, dataset, vecOfChannels[i],
paste("Distribution of Data (", i, ")", sep=""), 2, 0)
}else{
stuff<-plotHistoPerscreen(header, dataset, vecOfChannels[i],
paste("Distribution of norm. Data (", flag, ") (", i, ")", sep=""), 2, 0)
}
}else{
if (flag == 0){
stuff<-plotControlHistoPerscreen(header, dataset, vecOfChannels[i],
paste("Distribution of Data and Controls (", i, ")", sep=""), 2, 0)
}else{
stuff<-plotControlHistoPerscreen(header, dataset, vecOfChannels[i],
paste("Distribution of norm. Data (", flag, ") and Controls (", i, ")",
sep=""), 2, 0)
}
}
write.table(paste("<BR><BR><CENTER><TABLE border=0><TR>", sep=""), file=subPage,
append=T, quote=F, row.names=F, col.names=F)
write.table("<TH BGCOLOR=\"#e0e0ff\"></TH>", file=subPage, append=T, quote=F,
row.names=F, col.names=F)
for (j in stuff[[2]]:stuff[[3]]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Exp. ", j, "</TH>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subPage, append=T, quote=F, row.names=F, col.names=F)
write.table(paste("<TR><TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
for (j in stuff[[2]]:stuff[[3]]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", subPageClip, j,
".html\"><IMG SRC=\"", stuff[[1]], "(Exp. ", j,
").png\"/></A></CENTER><BR></TD>", sep=""), file=subPage, append=T,
quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=subPage, append=T, quote=F,
row.names=F, col.names=F)
}
for (i in stuff[[2]]:stuff[[3]]){
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file=paste(subPageClip, i, ".html", sep=""),
quote=F, row.names=F, col.names=F)
write.table(paste("<CENTER><H2>Distribution of data per plate for experiment ",
i, "</H2></CENTER>", sep=""), file=paste(subPageClip, i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><BR><CENTER><TABLE border=0><TR>", file=paste(subPageClip, i,
".html", sep=""), append=T, quote=F, row.names=F, col.names=F)
for (j in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", j, "</TH>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
}
write.table("</TR>", file=paste(subPageClip, i, ".html", sep=""), append=T,
quote=F, row.names=F, col.names=F)
write.table("<TR>", file=paste(subPageClip, i, ".html", sep=""), append=T,
quote=F, row.names=F, col.names=F)
for (j in 1:length(vecOfChannels)){
if (posNegFlag == 0){
if (flag == 0){
zeugs<-plotHistoPerscreen(header, dataset, vecOfChannels[j],
paste("Distribution of Data (", j, ")", sep=""), 2, 0)
}else{
zeugs<-plotHistoPerscreen(header, dataset, vecOfChannels[j],
paste("Distribution of norm. Data (", flag, ") (", j, ")", sep=""), 2, 0)
}
}else{
if (flag == 0){
zeugs<-plotControlHistoPerscreen(header, dataset, vecOfChannels[j],
paste("Distribution of Data and Controls (", j, ")", sep=""), 2, 0)
}else{
zeugs<-plotControlHistoPerscreen(header, dataset, vecOfChannels[j],
paste("Distribution of norm. Data (", flag, ") and Controls (", j, ")",
sep=""), 2, 0)
}
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", zeugs[[1]],
"(Exp. ", i, ").pdf\"><IMG SRC=\"", zeugs[[1]], "(Exp. ", i,
").png\"/></A></CENTER><BR></TD>", sep=""), file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
for (o in 1:length(vecOfChannels)){
if (posNegFlag == 0){
if (flag == 0){
stuff2<-plotHistoPerplate(header, dataset, vecOfChannels[o],
paste("Distribution of Data (", o, ")", sep=""), 2, 0)
}else{
stuff2<-plotHistoPerplate(header, dataset, vecOfChannels[o],
paste("Distribution of norm. Data (", flag, ") (", o, ")", sep=""), 2, 0)
}
}else{
if (flag == 0){
stuff2<-plotControlHistoPerplate(header, dataset, vecOfChannels[o],
paste("Distribution of Data and Controls (", o, ")", sep=""), 2, 0)
}else{
stuff2<-plotControlHistoPerplate(header, dataset, vecOfChannels[o],
paste("Distribution of norm. Data (", flag, ") and Controls (", o, ")",
sep=""), 2, 0)
}
}
write.table(paste("<BR><BR><CENTER><TABLE border=0><TR>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
write.table("<TH BGCOLOR=\"#e0e0ff\"></TH>", file=paste(subPageClip, i,
".html", sep=""), append=T, quote=F, row.names=F, col.names=F)
for (j in stuff2[[3]][1]:stuff2[[3]][2]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Plate ", j, "</TH>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F, row.names=F,
col.names=F)
}
write.table("</TR>", file=paste(subPageClip, i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
write.table(paste("<TR><TH BGCOLOR=\"#e0e0ff\">Channel ", o, "</TH>",
sep=""), file=paste(subPageClip, i, ".html", sep=""), append=T,
quote=F, row.names=F, col.names=F)
for (j in stuff2[[3]][1]:stuff2[[3]][2]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", stuff2[[1]],
"_Exp_", i, "_PerPlate_", j, "_.pdf\"><IMG SRC=\"", stuff2[[1]], "_Exp_", i,
"_PerPlate_", j, "_.png\"/></A></CENTER><BR></TD>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
}
}
}
function4a<-function(header, dataset, vecOfChannels, posNegFlag, firstLineBis,
secondLineBis, indexOutput, subPage, flag){
##########
####4a####
##########
subPageClip1<-strsplit(subPage, ".html")
subPageClip<-subPageClip1[[1]][1]
subPageClip<-paste(subPageClip, "_", sep="")
if (posNegFlag == 1){
write.table("<BR><BR><BR><CENTER><H2>Distribution of controls</H2></CENTER>",
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><CENTER><TABLE border=0><TR>", file=indexOutput, append=T,
quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
write.table("<TR>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
for (i in 1:length(vecOfChannels)){
if (flag == 0){
zeugs<-controlDensity(header, dataset, vecOfChannels[i],
paste("Control density (", i, ")", sep=""), 0, 1)
}else{
zeugs<-controlDensity(header, dataset, vecOfChannels[i],
paste("norm. Control density (", flag, ") (", i, ")", sep=""), 0, 1)
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", subPage,
"\"><IMG SRC=\"", zeugs, ".png\"/></A></CENTER><BR></TD>", sep=""),
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=indexOutput, append=T, quote=F,
row.names=F, col.names=F)
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file=subPage, quote=F, row.names=F, col.names=F)
write.table("<CENTER><H2>Control density per experiment</H2></CENTER>",
file=subPage, append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><BR><CENTER><TABLE border=0><TR>", file=subPage,
append=T, quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subPage, append=T, quote=F, row.names=F,
col.names=F)
write.table("<TR>", file=subPage, append=T, quote=F, row.names=F,
col.names=F)
for (i in 1:length(vecOfChannels)){
if (flag == 0){
zeugs<-controlDensity(header, dataset, vecOfChannels[i],
paste("Control density (", i, ")", sep=""), 0, 1)
}else{
zeugs<-controlDensity(header, dataset, vecOfChannels[i],
paste("norm. Control density (", flag, ") (", i, ")", sep=""), 0, 1)
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", zeugs,
".pdf\"><IMG SRC=\"", zeugs, ".png\"/></A></CENTER><BR></TD>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=subPage, append=T, quote=F,
row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
if (flag == 0){
stuff<-controlDensityPerScreen(header, dataset, vecOfChannels[i],
paste("Control density (", i, ")", sep=""), 0, 1)
}else{
stuff<-controlDensityPerScreen(header, dataset, vecOfChannels[i],
paste("norm. Control density (", flag, ") (", i, ")", sep=""), 0, 1)
}
write.table(paste("<BR><BR><CENTER><TABLE border=0><TR>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
write.table("<TH BGCOLOR=\"#e0e0ff\"></TH>", file=subPage, append=T,
quote=F, row.names=F, col.names=F)
for (j in stuff[[2]]:stuff[[3]]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Exp. ", j, "</TH>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subPage, append=T, quote=F, row.names=F, col.names=F)
write.table(paste("<TR><TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
for (j in stuff[[2]]:stuff[[3]]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", subPageClip, j,
".html\"><IMG SRC=\"", stuff[[1]], "(Exp. ", j,
").png\"/></A></CENTER><BR></TD>", sep=""), file=subPage, append=T,
quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=subPage, append=T, quote=F,
row.names=F, col.names=F)
}
for (i in stuff[[2]]:stuff[[3]]){
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file=paste(subPageClip, i, ".html", sep=""),
quote=F, row.names=F, col.names=F)
write.table(paste("<CENTER><H2>Control density per plate for experiment ", i,
"</H2></CENTER>", sep=""), file=paste(subPageClip, i, ".html", sep=""),
append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><BR><CENTER><TABLE border=0><TR>", file=paste(subPageClip, i,
".html", sep=""), append=T, quote=F, row.names=F, col.names=F)
for (j in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", j, "</TH>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
}
write.table("</TR>", file=paste(subPageClip, i, ".html", sep=""), append=T,
quote=F, row.names=F, col.names=F)
write.table("<TR>", file=paste(subPageClip, i, ".html", sep=""), append=T,
quote=F, row.names=F, col.names=F)
for (j in 1:length(vecOfChannels)){
if (flag == 0){
zeugs<-controlDensityPerScreen(header, dataset, vecOfChannels[j],
paste("Control density (", j, ")", sep=""), 0, 1)
}else{
zeugs<-controlDensityPerScreen(header, dataset, vecOfChannels[j],
paste("norm. Control density (", flag, ") (", j, ")", sep=""), 0, 1)
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", zeugs[[1]],
"(Exp. ", i, ").pdf\"><IMG SRC=\"", zeugs[[1]], "(Exp. ", i,
").png\"/></A></CENTER><BR></TD>", sep=""), file=paste(subPageClip, i,
".html", sep=""), append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
for (o in 1:length(vecOfChannels)){
if (flag == 0){
stuff2<-controlDensityPerPlate(header, dataset, vecOfChannels[o],
paste("Control density (", o, ")", sep=""), 2, 0, 1)
}else{
stuff2<-controlDensityPerPlate(header, dataset, vecOfChannels[o],
paste("norm. Control density (, ", flag, ") (", o, ")", sep=""), 2, 0, 1)
}
write.table(paste("<BR><BR><CENTER><TABLE border=0><TR>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
write.table("<TH BGCOLOR=\"#e0e0ff\"></TH>",
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
for (j in stuff2[[3]][1]:stuff2[[3]][2]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Plate ", j, "</TH>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
}
write.table("</TR>", file=paste(subPageClip, i, ".html", sep=""), append=T,
quote=F, row.names=F, col.names=F)
write.table(paste("<TR><TH BGCOLOR=\"#e0e0ff\">Channel ", o, "</TH>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
for (j in stuff2[[3]][1]:stuff2[[3]][2]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", stuff2[[1]],
"_Exp_", i, "_PerPlate_", j, "_.pdf\"><IMG SRC=\"", stuff2[[1]], "_Exp_", i,
"_PerPlate_", j, "_.png\"/></A></CENTER><BR></TD>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
}
}
}
}
function4b<-function(header, dataset, vecOfChannels, posNegFlag, firstLineBis,
secondLineBis, indexOutput, subPage, flag){
##########
####4b####
##########
if (posNegFlag == 1){
write.table("<BR><BR><BR><CENTER><H2>Z' Factors</H2></CENTER>",
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><CENTER><TABLE border=0><TR>", file=indexOutput,
append=T, quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
write.table("<TR>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
for (i in 1:length(vecOfChannels)){
if (flag == 0){
zeugs<-ZPRIMEQualControl(header, dataset, vecOfChannels[i],
paste("Z' Factors (", i, ")", sep=""), 0)
}else{
zeugs<-ZPRIMEQualControl(header, dataset, vecOfChannels[i],
paste("Z' Factors (", flag, ") (", i, ") (norm.)", sep=""), 0)
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", subPage,
"\"><IMG SRC=\"", zeugs[[1]], ".png\"/></A></CENTER><BR></TD>", sep=""),
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=indexOutput, append=T, quote=F,
row.names=F, col.names=F)
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file=subPage, quote=F, row.names=F, col.names=F)
write.table("<CENTER><H2>Z' Factors</H2></CENTER>", file=subPage, append=T,
quote=F, row.names=F, col.names=F)
write.table("<BR><BR><CENTER><TABLE border=0><TR>", file=subPage, append=T,
quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""), file=subPage,
append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subPage, append=T, quote=F, row.names=F, col.names=F)
write.table("<TR>", file=subPage, append=T, quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
if (flag == 0){
zeugs<-ZPRIMEQualControl(header, dataset, vecOfChannels[i],
paste("Z' Factors (", i, ")", sep=""), 0)
}else{
zeugs<-ZPRIMEQualControl(header, dataset, vecOfChannels[i],
paste("Z' Factors (", flag, ") (", i, ") (norm.)", sep=""), 0)
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", zeugs[[1]],
".pdf\"><IMG SRC=\"", zeugs[[1]], ".png\"/></A></CENTER><BR></TD>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=subPage, append=T, quote=F,
row.names=F, col.names=F)
s1<-"<BR><BR><CENTER><TABLE border=0><TR><TH BGCOLOR=\"#d0d0f0\">"
s2<-"Exp. #</TH><TH BGCOLOR=\"#e0e0ff\">Plate #</TH>"
s3<-paste(s1, s2, sep="")
write.table(s3, file=subPage, append=T, quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#d0d0f0\">Z' Score Ch. ", i, "</TH>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subPage, append=T, quote=F, row.names=F, col.names=F)
for (i in 2:nrow(zeugs[[2]])){
write.table(paste("<TR><TD BGCOLOR=\"#e0e0f0\">", zeugs[[2]][i, 1],
"</TD><TD BGCOLOR=\"#f0f0ff\" align=center>", zeugs[[2]][i, 2], "</TD>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
for (j in 1:length(vecOfChannels)){
if (flag == 0){
zeugs<-ZPRIMEQualControl(header, dataset, vecOfChannels[j],
paste("Z' Factors (", j, ")", sep=""), 0)
}else{
zeugs<-ZPRIMEQualControl(header, dataset, vecOfChannels[j],
paste("Z' Factors (", flag, ") (", j, ") (norm.)", sep=""), 0)
}
write.table(paste("<TD BGCOLOR=\"#e0e0f0\" align=center>", zeugs[[2]][i, 3],
"</TD>", sep=""), file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subPage, append=T, quote=F, row.names=F,
col.names=F)
}
write.table("</TABLE></CENTER>", file=subPage, append=T, quote=F,
row.names=F, col.names=F)
}
}
function5<-function(header, dataset, vecOfChannels, posNegFlag, firstLineBis,
secondLineBis, indexOutput, subPage, flag){
#########
####5####
#########
subPageClip1<-strsplit(subPage, ".html")
subPageClip<-subPageClip1[[1]][1]
subPageClip<-paste(subPageClip, "_", sep="")
if (posNegFlag == 1){
write.table("<BR><BR><BR><CENTER><H2>Comparison of controls</H2></CENTER>",
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><CENTER><TABLE border=0><TR>", file=indexOutput, append=T,
quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
write.table("<TR>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
for (i in 1:length(vecOfChannels)){
if (flag == 0){
zeugs<-makeBoxplotControls(header, dataset, vecOfChannels[i],
paste("Comparison of controls (", i, ")", sep=""), 0)
}else{
zeugs<-makeBoxplotControls(header, dataset, vecOfChannels[i],
paste("Comparison of controls (", flag, ") (", i, ") (norm.)", sep=""), 0)
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", subPage,
"\"><IMG SRC=\"", zeugs, ".png\"/></A></CENTER><BR></TD>", sep=""),
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=indexOutput, append=T, quote=F,
row.names=F, col.names=F)
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file=subPage, quote=F, row.names=F, col.names=F)
write.table("<CENTER><H2>Comparison of controls per experiment<H2></CENTER>",
file=subPage, append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><BR><CENTER><TABLE border=0><TR>", file=subPage, append=T,
quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subPage, append=T, quote=F, row.names=F, col.names=F)
write.table("<TR>", file=subPage, append=T, quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
if (flag == 0){
zeugs<-makeBoxplotControls(header, dataset, vecOfChannels[i],
paste("Comparison of controls (", i, ")", sep=""), 0)
}else{
zeugs<-makeBoxplotControls(header, dataset, vecOfChannels[i],
paste("Comparison of controls (", flag, ") (", i, ") (norm.)", sep=""), 0)
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", zeugs,
".pdf\"><IMG SRC=\"", zeugs, ".png\"/></A></CENTER><BR></TD>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=subPage, append=T, quote=F,
row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
if (flag == 0){
stuff<-makeBoxplotControlsPerScreen(header, dataset, vecOfChannels[i],
paste("Comparison of controls (", i, ")", sep=""), 2, 0)
}else{
stuff<-makeBoxplotControlsPerScreen(header, dataset, vecOfChannels[i],
paste("Comparison of controls (", flag, ") (", i, ") (norm.)", sep=""), 2, 0)
}
write.table(paste("<BR><BR><CENTER><TABLE border=0><TR>", sep=""), file=subPage,
append=T, quote=F, row.names=F, col.names=F)
write.table("<TH BGCOLOR=\"#e0e0ff\"></TH>", file=subPage, append=T, quote=F,
row.names=F, col.names=F)
for (j in stuff[[2]]:stuff[[3]]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Exp. ", j, "</TH>", sep=""), file=subPage,
append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subPage, append=T, quote=F, row.names=F, col.names=F)
write.table(paste("<TR><TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
for (j in stuff[[2]]:stuff[[3]]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", subPageClip, j,
".html\"><IMG SRC=\"", stuff[[1]], " (Exp.", j,
").png\"/></A></CENTER><BR></TD>", sep=""), file=subPage, append=T, quote=F,
row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=subPage, append=T, quote=F,
row.names=F, col.names=F)
}
for (i in stuff[[2]]:stuff[[3]]){
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file=paste(subPageClip, i, ".html", sep=""),
quote=F, row.names=F, col.names=F)
s1<-"<CENTER><H2>Comparison of controls per plate for experiment "
s2<-"</H2></CENTER>"
write.table(paste(s1, i, s2, sep=""), file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><BR><CENTER><TABLE border=0><TR>", file=paste(subPageClip, i,
".html", sep=""), append=T, quote=F, row.names=F, col.names=F)
for (j in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", j, "</TH>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
}
write.table("</TR>", file=paste(subPageClip, i, ".html", sep=""), append=T,
quote=F, row.names=F, col.names=F)
write.table("<TR>", file=paste(subPageClip, i, ".html", sep=""), append=T,
quote=F, row.names=F, col.names=F)
for (j in 1:length(vecOfChannels)){
if (flag == 0){
zeugs<-makeBoxplotControlsPerScreen(header, dataset, vecOfChannels[j],
paste("Comparison of controls (", j, ")", sep=""), 2, 0)
}else{
zeugs<-makeBoxplotControlsPerScreen(header, dataset, vecOfChannels[j],
paste("Comparison of controls (", flag, ") (", j, ") (norm.)", sep=""), 2, 0)
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", zeugs[[1]],
" (Exp.", i, ").pdf\"><IMG SRC=\"", zeugs[[1]], " (Exp.", i,
").png\"/></A></CENTER><BR></TD>", sep=""), file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
for (o in 1:length(vecOfChannels)){
if (flag == 0){
stuff2<-makeBoxplotControlsPerPlate(header, dataset, vecOfChannels[o],
paste("Comparison of controls (", o, ")", sep=""), 2, 0)
}else{
stuff2<-makeBoxplotControlsPerPlate(header, dataset, vecOfChannels[o],
paste("Comparison of controls (", flag, ") (", o, ") (norm.)", sep=""), 2, 0)
}
write.table(paste("<BR><BR><CENTER><TABLE border=0><TR>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
write.table("<TH BGCOLOR=\"#e0e0ff\"></TH>", file=paste(subPageClip, i,
".html", sep=""), append=T, quote=F, row.names=F, col.names=F)
for (j in stuff2[[3]][1]:stuff2[[3]][2]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Plate ", j, "</TH>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
}
write.table("</TR>", file=paste(subPageClip, i, ".html", sep=""), append=T,
quote=F, row.names=F, col.names=F)
write.table(paste("<TR><TH BGCOLOR=\"#e0e0ff\">Channel ", o, "</TH>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
for (j in stuff2[[3]][1]:stuff2[[3]][2]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", stuff2[[1]],
"_Exp_", i, "_PerPlate", j, ".pdf\"><IMG SRC=\"", stuff2[[1]], "_Exp_", i,
"_PerPlate", j, ".png\"/></A></CENTER><BR></TD>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
}
}
}
}
function6<-function(header, dataset, vecOfChannels, firstLineBis,
secondLineBis, indexOutput, subPage, flag){
#########
####6####
#########
subPageClip1<-strsplit(subPage, ".html")
subPageClip<-subPageClip1[[1]][1]
subPageClip<-paste(subPageClip, "_", sep="")
write.table("<BR><BR><BR><CENTER><H2>QQ plots</H2></CENTER>", file=indexOutput,
append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><CENTER><TABLE border=0><TR>", file=indexOutput, append=T,
quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
write.table("<TR>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
for (i in 1:length(vecOfChannels)){
if (flag == 0){
zeugs<-plotQQ(header, dataset, vecOfChannels[i], paste("QQ plot (", i, ")",
sep=""), 0)
}else{
zeugs<-plotQQ(header, dataset, vecOfChannels[i], paste("QQ plot (", flag,
") (", i, ") (norm.)", sep=""), 0)
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", subPage,
"\"><IMG SRC=\"", zeugs, ".png\"/></A></CENTER><BR></TD>", sep=""),
file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=indexOutput, append=T, quote=F,
row.names=F, col.names=F)
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file=subPage, quote=F, row.names=F, col.names=F)
write.table("<CENTER><H2>QQ plots per experiment</H2></CENTER>", file=subPage,
append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><BR><CENTER><TABLE border=0><TR>", file=subPage, append=T,
quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subPage, append=T, quote=F, row.names=F,
col.names=F)
write.table("<TR>", file=subPage, append=T, quote=F, row.names=F,
col.names=F)
for (i in 1:length(vecOfChannels)){
if (flag == 0){
zeugs<-plotQQ(header, dataset, vecOfChannels[i], paste("QQ plot (",
i, ")", sep=""), 0)
}else{
zeugs<-plotQQ(header, dataset, vecOfChannels[i], paste("QQ plot (",
flag, ") (", i, ") (norm.)", sep=""), 0)
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", zeugs,
".pdf\"><IMG SRC=\"", zeugs, ".png\"/></A></CENTER><BR></TD>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=subPage, append=T, quote=F,
row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
if (flag == 0){
stuff<-plotQQperscreen(header, dataset, vecOfChannels[i], paste("QQ plot (",
i, ")", sep=""), 2, 0)
}else{
stuff<-plotQQperscreen(header, dataset, vecOfChannels[i], paste("QQ plot (",
flag, ") (", i, ") (norm.)", sep=""), 2, 0)
}
write.table(paste("<BR><BR><CENTER><TABLE border=0><TR>", sep=""), file=subPage,
append=T, quote=F, row.names=F, col.names=F)
write.table("<TH BGCOLOR=\"#e0e0ff\"></TH>", file=subPage, append=T, quote=F,
row.names=F, col.names=F)
for (j in stuff[[2]]:stuff[[3]]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Exp. ", j, "</TH>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subPage, append=T, quote=F, row.names=F, col.names=F)
write.table(paste("<TR><TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=subPage, append=T, quote=F, row.names=F, col.names=F)
for (j in stuff[[2]]:stuff[[3]]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", subPageClip, j,
".html\"><IMG SRC=\"", stuff[[1]], " (Exp.", j,
").png\"/></A></CENTER><BR></TD>", sep=""), file=subPage, append=T, quote=F,
row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=subPage, append=T,
quote=F, row.names=F, col.names=F)
}
for (i in stuff[[2]]:stuff[[3]]){
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file=paste(subPageClip, i, ".html", sep=""),
quote=F, row.names=F, col.names=F)
s1<-"<CENTER><H2>Comparison of controls per plate for experiment "
s2<-"</H2></CENTER>"
write.table(paste(s1, i, s2, sep=""), file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><BR><CENTER><TABLE border=0><TR>", file=paste(subPageClip, i,
".html", sep=""), append=T, quote=F, row.names=F, col.names=F)
for (j in 1:length(vecOfChannels)){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Channel ", j, "</TH>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F, row.names=F,
col.names=F)
}
write.table("</TR>", file=paste(subPageClip, i, ".html", sep=""), append=T,
quote=F, row.names=F, col.names=F)
write.table("<TR>", file=paste(subPageClip, i, ".html", sep=""), append=T,
quote=F, row.names=F, col.names=F)
for (j in 1:length(vecOfChannels)){
if (flag == 0){
zeugs<-plotQQperscreen(header, dataset, vecOfChannels[j], paste("QQ plot (", j,
")", sep=""), 2, 0)
}else{
zeugs<-plotQQperscreen(header, dataset, vecOfChannels[j], paste("QQ plot (",
flag, ") (", j, ") (norm.)", sep=""), 2, 0)
}
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", zeugs[[1]],
" (Exp.", i, ").pdf\"><IMG SRC=\"", zeugs[[1]], " (Exp.", i,
").png\"/></A></CENTER><BR></TD>", sep=""), file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
for (o in 1:length(vecOfChannels)){
if (flag == 0){
stuff2<-plotQQperplate(header, dataset, vecOfChannels[o], paste("QQ plot (", o,
")", sep=""), 2, 0)
}else{
stuff2<-plotQQperplate(header, dataset, vecOfChannels[o], paste("QQ plot (",
flag, ") (", o, ") (norm.)", sep=""), 2, 0)
}
write.table(paste("<BR><BR><CENTER><TABLE border=0><TR>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
write.table("<TH BGCOLOR=\"#e0e0ff\"></TH>", file=paste(subPageClip, i,
".html", sep=""), append=T, quote=F, row.names=F, col.names=F)
for (j in stuff2[[3]][1]:stuff2[[3]][2]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Plate ", j, "</TH>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
}
write.table("</TR>", file=paste(subPageClip, i, ".html", sep=""), append=T,
quote=F, row.names=F, col.names=F)
write.table(paste("<TR><TH BGCOLOR=\"#e0e0ff\">Channel ", o, "</TH>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
for (j in stuff2[[3]][1]:stuff2[[3]][2]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", stuff2[[1]],
"Exp", i, "_PerPlate", j, ".pdf\"><IMG SRC=\"", stuff2[[1]], "Exp", i,
"_PerPlate", j, ".png\"/></A></CENTER><BR></TD>", sep=""),
file=paste(subPageClip, i, ".html", sep=""), append=T, quote=F,
row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=paste(subPageClip, i, ".html",
sep=""), append=T, quote=F, row.names=F, col.names=F)
}
}
}
function7<-function(header, dataset, vecOfChannels, firstLineBis,
secondLineBis, indexOutput, subpageA, subpageB, flag, flagForNorm){
#########
####7####
#########
s1<-"<BR><BR><BR><CENTER><H2>Spearmans correlation coefficients</H2></CENTER>"
write.table(s1, file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
write.table("<BR><CENTER><TABLE border=0><TR>", file=indexOutput, append=T,
quote=F, row.names=F, col.names=F)
if (flag == 1){
for (j in 1:2){
for (i in 1:length(vecOfChannels)){
write.table(paste("<TH>Channel", i, "</TH>", sep=""), file=indexOutput,
append=T, quote=F, row.names=F, col.names=F)
}
}
}else{
for (i in 1:length(vecOfChannels)){
write.table(paste("<TH>Channel", i, "</TH>", sep=""), file=indexOutput,
append=T, quote=F, row.names=F, col.names=F)
}
}
write.table("</TR><TR>", file=indexOutput, append=T, quote=F,
row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
write.table("<TD>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
tableOfCoeffs<-replicatesSpearmancor(header, dataset, 1, vecOfChannels[i],
"GeneName", "per_experiment")
s2<-"<CENTER><TABLE border=0><TR><TH BGCOLOR=\"#d0d0f0\"></TH><TH BGCOLOR="
s3<-"\"#e0e0ff\">Rep. 1 vs. 2</TH><TH BGCOLOR=\"#d0d0f0\">Rep. 2 vs. 3</TH>"
s4<-"<TH BGCOLOR=\"#e0e0ff\">Rep. 1 vs. 3</TH></TR>"
s5<-paste(s2, s3, s4, sep="")
write.table(s5, file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
counter<-1
for (j in 1:max(tableOfCoeffs[, 1])){
write.table(paste("<TR><TD BGCOLOR=\"#e0e0f0\">Exp. ", j,
"</TD><TD BGCOLOR=\"#f0f0ff\" align=center>", tableOfCoeffs[counter, 4],
"</TD><TD BGCOLOR=\"#e0e0f0\" align=center>", tableOfCoeffs[(counter+1), 4],
"</TD><TD BGCOLOR=\"#f0f0ff\" align=center>", tableOfCoeffs[(counter+2), 4],
"</TD></TR>", sep=""), file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
counter<-counter+3
}
write.table("</CENTER></TABLE>", file=indexOutput, append=T, quote=F,
row.names=F, col.names=F)
write.table("</TD>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
}
if (flag == 1){
for (i in 1:length(vecOfChannels)){
write.table("<TD>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
tableOfCoeffs<-replicatesSpearmancor(header, dataset, 2, vecOfChannels[i],
"GeneName", "between_experiments")
s6<-"<CENTER><TABLE border=0><TR><TH BGCOLOR=\"#d0d0f0\">Exp.</TH><TH BGCOLOR="
s7<-"\"#e0e0ff\">Exp.</TH><TH BGCOLOR=\"#d0d0f0\">Correlation coeff.</TH></TR>"
s8<-paste(s6, s7, sep="")
write.table(s8, file=indexOutput, append=T, quote=F, row.names=F, col.names=F)
for (j in 1:nrow(tableOfCoeffs)){
write.table(paste("<TR><TD BGCOLOR=\"#e0e0f0\">", tableOfCoeffs[j, 1],
"</TD><TD BGCOLOR=\"#f0f0ff\" align=center>", tableOfCoeffs[j, 2],
"</TD><TD BGCOLOR=\"#e0e0f0\" align=center>", tableOfCoeffs[j, 3],
"</TD></TR>", sep=""), file=indexOutput, append=T, quote=F,
row.names=F, col.names=F)
}
write.table("</CENTER></TABLE>", file=indexOutput, append=T, quote=F,
row.names=F, col.names=F)
write.table("</TD>", file=indexOutput, append=T, quote=F, row.names=F,
col.names=F)
}
}
write.table("</TR></CENTER></TABLE>", file=indexOutput, append=T, quote=F,
row.names=F, col.names=F)
s9<-"<A HREF=\""
s1<-"\">Correlation of variation plots</A>, <A HREF=\""
s2<-"\">Plots for replicate comparison</A>"
write.table(paste(s9, subpageA, s1, subpageB, s2, sep=""), file=indexOutput,
append=T, quote=F, row.names=F, col.names=F)
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file=subpageA, quote=F, row.names=F, col.names=F)
write.table("<CENTER><H2>Correlation of variation</H2></CENTER>", file=subpageA,
append=T, quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
stuff<-replicatesCV(header, dataset, paste("Correlation of variation (",
flagForNorm, ") (", i, ")", sep=""), vecOfChannels[i], "GeneName", 2, 0)
write.table(paste("<BR><BR><CENTER><TABLE border=0><TR>", sep=""),
file=subpageA, append=T, quote=F, row.names=F, col.names=F)
write.table("<TH BGCOLOR=\"#e0e0ff\"></TH>", file=subpageA, append=T, quote=F,
row.names=F, col.names=F)
for (j in stuff[[2]]:stuff[[3]]){
write.table(paste("<TH BGCOLOR=\"#e0e0ff\">Exp. ", j, "</TH>", sep=""),
file=subpageA, append=T, quote=F, row.names=F, col.names=F)
}
write.table("</TR>", file=subpageA, append=T, quote=F, row.names=F, col.names=F)
write.table(paste("<TR><TH BGCOLOR=\"#e0e0ff\">Channel ", i, "</TH>", sep=""),
file=subpageA, append=T, quote=F, row.names=F, col.names=F)
for (j in stuff[[2]]:stuff[[3]]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", stuff[[1]],
" (Exp.", j, ").pdf\"><IMG SRC=\"", stuff[[1]], " (Exp.", j,
").png\"/></A></CENTER><BR></TD>", sep=""), file=subpageA, append=T,
quote=F, row.names=F, col.names=F)
}
write.table("</TR></CENTER></TABLE>", file=subpageA, append=T, quote=F,
row.names=F, col.names=F)
}
write.table(paste("<HTML><HEAD><TITLE>", secondLineBis, ", ", firstLineBis,
"</TITLE></HEAD>", sep=""), file=subpageB, quote=F, row.names=F, col.names=F)
write.table("<CENTER><H2>Comparison of replicates</H2></CENTER>",
file=subpageB, append=T, quote=F, row.names=F, col.names=F)
for (i in 1:length(vecOfChannels)){
if (i>1){
write.table("<BR>", file=subpageB, append=T, quote=F, row.names=F, col.names=F)
}
write.table(paste("<BR><CENTER>Channel ", i, "</CENTER>", sep=""),
file=subpageB, append=T, quote=F, row.names=F, col.names=F)
stuff<-compareReplicates(header, dataset, paste("Comparison of replicates (",
flagForNorm, ") (", i, ")", sep=""), vecOfChannels[i], "GeneName", 2, 0)
for (j in stuff[[2]]:stuff[[3]]){
write.table(paste("<CENTER><TABLE border=0><TR><TH BGCOLOR=\"#e0e0ff\">Exp.",
j, "</TH>", sep=""), file=subpageB, append=T, quote=F, row.names=F, col.names=F)
for (k in 1:stuff[[4]]){
write.table(paste("<TD BGCOLOR=\"#f0f0ff\"><CENTER><A HREF=\"", stuff[[1]],
"_Exp_", j, "(", k, ").pdf\"><IMG SRC=\"", stuff[[1]], "_Exp_", j, "(", k,
").png\"/></A></CENTER><BR></TD>", sep=""), file=subpageB, append=T, quote=F,
row.names=F, col.names=F)
}
}
write.table("</TR></CENTER></TABLE>", file=subpageB, append=T, quote=F,
row.names=F, col.names=F)
}
}
vennDiagfunc<-function(hitVectors, hitVectorsTestNames, hitScoringVec1,
listOfArgs4stat){
typeOfScoringVec<-rep(NA_character_, length(hitVectors))
typeOfComparison<-rep(NA_character_, length(hitVectors))
saveif<-0
if (hitScoringVec1[1] == 1){
for (i in 1:length(hitVectorsTestNames)){
if (hitVectorsTestNames[[i]] == "t test"
| hitVectorsTestNames[[i]] == "Mann-Whitney test"){
if (listOfArgs4stat[[i]][1] == "l"){
typeOfScoringVec[i]<-"l"
typeOfComparison[i]<-"P"
}
if (listOfArgs4stat[[i]][1] == "g"){
typeOfScoringVec[i]<-"g"
typeOfComparison[i]<-"P"
}
if (listOfArgs4stat[[i]][1] == "two.sided"){
typeOfScoringVec[i]<-"two.sided"
typeOfComparison[i]<-"P"
}
}
if (hitVectorsTestNames[[i]] == "Rank product test"){
if (listOfArgs4stat[[i]][2] == 1){
typeOfScoringVec[i]<-"l"
typeOfComparison[i]<-"P"
}else{
typeOfScoringVec[i]<-"g"
typeOfComparison[i]<-"P"
}
}
}
}
if (hitScoringVec1[2] == 1 | hitScoringVec1[2] == 2){
saveif<-length(which(typeOfScoringVec == "l"))
for (g in 1:saveif){
if(sum(is.na(typeOfScoringVec))!=0){
##if there are NAs in typeOfScoringVec
ind<-min(which(is.na(typeOfScoringVec)))
typeOfScoringVec[ind]<-"l"
if (hitScoringVec1[2] == 1){
typeOfComparison[ind]<-"Z"
}
if (hitScoringVec1[2] == 2){
typeOfComparison[ind]<-"PZ"
}
}
}
}
if (hitScoringVec1[3] == 1 | hitScoringVec1[3] == 2){
saveif<-length(which(typeOfScoringVec == "g"))
for (g in 1:saveif){
if(sum(is.na(typeOfScoringVec))!=0){
##if there are NAs in typeOfScoringVec
ind<-min(which(is.na(typeOfScoringVec)))
typeOfScoringVec[ind]<-"g"
if (hitScoringVec1[3] == 1){
typeOfComparison[ind]<-"Z"
}
if (hitScoringVec1[3] == 2){
typeOfComparison[ind]<-"PZ"
}
}
}
}
invisible(list(typeOfScoringVec, typeOfComparison))
}
listChooseIndex<-function(fullList, chooseVec){
for (g in 1:length(chooseVec)){
if (g == 1){
partList<-list(fullList[[chooseVec[g]]])
}else{
partList[[g]]<-fullList[[chooseVec[g]]]
}
}
invisible(partList)
}
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