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R/Visualisation.R
In qfa: Tools for Quantitative Fitness Analysis (QFA) of Arrayed Microbial Cultures Growing on Solid Agar Surfaces
Defines functions
makeVisTool
complexesFromSource
buildComplexes
buildBenschop
iRVisDemo
NAtoBlank
getResults
toClipboard
buildGO
buildPombeGO
getText
drawSel
printSelected
reportExpts
Documented in
buildBenschop
buildComplexes
buildGO
buildPombeGO
complexesFromSource
drawSel
getResults
getText
iRVisDemo
makeVisTool
NAtoBlank
printSelected
reportExpts
toClipboard
# Huge function closure to keep visualisation tool environment out of global environment and keep CRAN happy
makeVisTool=function(){
globs<-new.env()
# Plotting function
epiplot<-function(results,qthresh,fitratio=FALSE,ref.orf="YOR202W",xxlab="Control Fitness",yylab="Query Fitness",mmain="Epistasis Plot",ymin=0,ymax=0,xmin=0,xmax=0,ecol="green",scol="red",esym=19,ssym=19,reg="lmreg"){
enhancers<-gethits(results,qthresh,type="E")
suppressors<-gethits(results,qthresh,type="S")
others<-results[(!results$ORF%in%enhancers$ORF)&(!results$ORF%in%suppressors$ORF),]
plot(NULL,type="n",xlim=c(xmin,xmax),ylim=c(ymin,ymax),
xlab=xxlab,ylab=yylab,main=mmain,
col=8,pch=19,cex=0.5)
# Add line for genetic independence
if (fitratio!=FALSE){abline(0,fitratio,lwd=2,col=8)} else {
slp=lm.epi(results$QueryFitnessSummary,results$ControlFitnessSummary,modcheck=FALSE,reg="lmreg")
abline(0,slp,lwd=2,col=8)}
# Add 1:1 fitness line
abline(0,1,lwd=2,lty=4,col=8)
# Add reference ORF fitnesses lines
if (ref.orf!=FALSE){
reforf<-results[results$ORF==ref.orf,]
abline(v=reforf$ControlFitnessSummary,col="lightblue",lwd=2)
abline(h=reforf$QueryFitnessSummary,col="lightblue",lwd=2)}
# Add points for non-suppressors & non-enhancers
points(others$ControlFitnessSummary,others$QueryFitnessSummary,col="grey",cex=0.75,pch=19)
#text(others$ControlFitnessSummary,others$QueryFitnessSummary,others$Gene,col="grey",pos=4,offset=0.1,cex=0.4)
# Add suppressors & enhancers
if(length(enhancers$ORF)>0){
points(enhancers$ControlFitnessSummary,enhancers$QueryFitnessSummary,col=ecol,bg=ecol,pch=esym,cex=0.75)
#text(enhancers$ControlFitnessSummary,enhancers$QueryFitnessSummary,enhancers$Gene,col=1,pos=4,offset=0.1,cex=0.4)
}
if(length(suppressors$ORF)>0){
points(suppressors$ControlFitnessSummary,suppressors$QueryFitnessSummary,col=scol,bg=scol,pch=ssym,cex=0.75)
#text(suppressors$ControlFitnessSummary,suppressors$QueryFitnessSummary,suppressors$Gene,col=1,pos=4,offset=0.1,cex=0.4)
}
}
makePlot=function(datno,focusPlot=TRUE,...){
if(globs$compno>0){
lst=strsplit(globs$GROUPS$GroupORFs[globs$compno]," ")[[1]]
Ngrp=paste("(N=",length(lst),")",sep="")
compnm=paste("Group",paste(globs$compno,":",sep=""),globs$GROUPS$GroupName[globs$compno],Ngrp,globs$GROUPS$GroupID[globs$compno])
}else{
compnm=""
}
#plotdesc=paste(globs$datlist[[datno]]$datname,globs$datlist[[datno]]$cScrNm,globs$datlist[[datno]]$cTreat,":",globs$datlist[[datno]]$qScrNm,globs$datlist[[datno]]$qTreat)
plotdesc=globs$datlist[[datno]]$datname
maintitle=paste(plotdesc,compnm,sep="\n")
if (globs$datlist[[datno]]$cCond=="") {ControlCondition=globs$datlist[[datno]]$cMed}else{ControlCondition=globs$datlist[[datno]]$cCond}
if (globs$datlist[[datno]]$qCond=="") {QueryCondition=globs$datlist[[datno]]$qMed}else{QueryCondition=globs$datlist[[datno]]$qCond}
xlab=paste(globs$datlist[[datno]]$cScrNm,globs$datlist[[datno]]$cTreat,ControlCondition,globs$datlist[[datno]]$cFit,globs$datlist[[datno]]$cInoc,globs$datlist[[datno]]$cScrID,globs$datlist[[datno]]$cCli,globs$datlist[[datno]]$cDate)
ylab=paste(globs$datlist[[datno]]$qScrNm,globs$datlist[[datno]]$qTreat,QueryCondition,globs$datlist[[datno]]$qFit,globs$datlist[[datno]]$qInoc,globs$datlist[[datno]]$qScrID,globs$datlist[[datno]]$qCli,globs$datlist[[datno]]$qDate)
globs$orftargs=globs$dat$ORF[globs$targs]
globs$dat=globs$datlist[[datno]]$res
globs$targs=match(toupper(globs$orftargs),toupper(globs$dat$ORF))
epiplot(globs$dat,0.05,mmain=maintitle,xxlab=xlab,yylab=ylab,ymin=globs$fymin[datno],ymax=globs$fymax[datno],xmin=globs$fxmin[datno],xmax=globs$fxmax[datno],reg=globs$reg,...)
if(globs$compno>0){
lst=strsplit(globs$GROUPS$GroupORFs[globs$compno]," ")[[1]]
dcomp=globs$dat[toupper(globs$dat$ORF)%in%toupper(lst),]
if(length(dcomp$ORF)>0){
points(dcomp$ControlFitnessSummary,dcomp$QueryFitnessSummary,col="purple",pch=16,cex=1.5)
text(dcomp$ControlFitnessSummary,dcomp$QueryFitnessSummary,dcomp$Gene,pos=sample(1:4,length(dcomp$Gene),replace=TRUE),cex=1.0)
}
}
if(length(globs$targs)>0){
points(globs$dat$ControlFitnessSummary[globs$targs],globs$dat$QueryFitnessSummary[globs$targs],col="blue",pch=16,cex=0.2)
text(globs$dat$ControlFitnessSummary[globs$targs],globs$dat$QueryFitnessSummary[globs$targs],globs$dat$Gene[globs$targs],pos=globs$posits,cex=0.75)
}
if ((Sys.info()['sysname']=="Windows")&focusPlot) bringToTop()
}
rnkPlot=function(datno,focusPlot=TRUE,qthresh=0.05,ecol="green",scol="red",esym=19,ssym=19){
if(globs$compno>0){
lst=strsplit(globs$GROUPS$GroupORFs[globs$compno]," ")[[1]]
Ngrp=paste("(N=",length(lst),")",sep="")
compnm=paste("Group",paste(globs$compno,":",sep=""),globs$GROUPS$GroupName[globs$compno],Ngrp,globs$GROUPS$GroupID[globs$compno])
}else{
compnm=""
}
maintitle=paste(globs$datlist[[datno]]$datname,compnm,sep="\n")
xlab=paste(globs$datlist[[datno]]$cScrID)
ylab=paste(globs$datlist[[datno]]$qScrID)
if(globs$ratploty=="ratio") {axislab=paste("Fit ",ylab,"/Fit ",xlab," (log scale)",sep=""); ratlog="y"}
if(globs$ratploty=="GIS") {axislab=paste("GIS ",ylab," vs. ",xlab," (linear scale)",sep=""); ratlog=""}
if(globs$ratploty=="QueryFitnessSummary") {axislab=paste("Query Fit ",ylab," (linear scale)",sep=""); ratlog=""}
if(globs$ratploty=="ControlFitnessSummary") {axislab=paste("Control Fit ",xlab," (linear scale)",sep=""); ratlog=""}
if(globs$ratploty=="QueryFitnessSummaryLOG") {axislab=paste("Query Fit ",ylab," (log scale)",sep=""); ratlog="y"}
if(globs$ratploty=="ControlFitnessSummaryLOG") {axislab=paste("Control Fit ",xlab," (log scale)",sep=""); ratlog="y"}
globs$orftargs=globs$dat$ORF[globs$targs]
if(globs$ind=="gindex") ratlab="Ranked by standard gene name (alphabetical order)"
if(globs$ind=="oindex") ratlab="Ranked by systematic gene name (chromosome coordinate)"
if(globs$ind=="cindex") ratlab="Ranked by control fitness"
if(globs$ind=="qindex") ratlab="Ranked by query fitness"
if(globs$ind=="rindex") ratlab="Ranked by query/control fitness ratio"
globs$dat=globs$datlist[[datno]]$res
globs$targs=match(globs$orftargs,globs$dat$ORF)
rply=gsub("LOG","",globs$ratploty)
plot(globs$dat[[globs$ind]],globs$dat[[rply]],xlab=ratlab,log=ratlog,ylab=axislab,main=maintitle,col="grey",cex=0.5,pch=19)
if(globs$compno>0){
lst=strsplit(globs$GROUPS$GroupORFs[globs$compno]," ")[[1]]
globs$dcomp=globs$dat[globs$dat$ORF%in%lst,]
if(length(globs$dcomp$ORF)>0){
points(globs$dcomp[[globs$ind]],globs$dcomp[[rply]],col="purple",pch=16,cex=1.5)
text(globs$dcomp[[globs$ind]],globs$dcomp[[rply]],globs$dcomp$Gene,pos=1,cex=1.0)
}
}
if(length(globs$targs)>0){
points(globs$dat[[globs$ind]][globs$targs],globs$dat[[rply]][globs$targs],col="blue",pch=16,cex=0.2)
text(globs$dat[[globs$ind]][globs$targs],globs$dat[[rply]][globs$targs],globs$dat$Gene[globs$targs],pos=globs$posits,cex=0.75)
}
if ((Sys.info()['sysname']=="Windows")&focusPlot) bringToTop()
}
targFun=function(x,y,datobj){
if(globs$rankPlot){
rply=gsub("LOG","",globs$ratploty)
if(globs$ratploty=="ratio"){
d=((x-datobj[[globs$ind]])/max(datobj[[globs$ind]]))^2+(y-datobj[[rply]])^2
}else{
d=(x/max(datobj[[globs$ind]])-datobj[[globs$ind]]/max(datobj[[globs$ind]]))^2+(y/max(datobj[[rply]])-datobj[[rply]]/max(datobj[[rply]]))^2
}
}else{
d=(x-datobj$ControlFitnessSummary)^2+(y-datobj$QueryFitnessSummary)^2
}
best=which.min(d)
return(best)
}
mouse=function(buttons,x,y){
if(0%in%buttons) {
# Problem with Cairo coordinate system here...
globs$xf=grconvertX(x,from="ndc",to="user")
globs$yf=grconvertY(y,from="ndc",to="user")
if(globs$zooming==TRUE){
if(identical(globs$zoomTL,c(-99,-99))) {
globs$zoomTL=c(globs$xf,globs$yf)
}else{
globs$zoomBR=c(globs$xf,globs$yf)
# Zoom in!
globs$fxmin[globs$datno]=globs$zoomTL[1]
globs$fxmax[globs$datno]=globs$zoomBR[1]
globs$fymin[globs$datno]=globs$zoomBR[2]
globs$fymax[globs$datno]=globs$zoomTL[2]
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}
# Reset zooming parameters
globs$zooming=FALSE
globs$zoomTL=c(-99,-99)
globs$zoomBR=c(-99,-99)
}
}else{
if(globs$sel==0){
# Find nearest gene, highlight location, draw plot
candidate=targFun(globs$xf,globs$yf,globs$dat)
if(!candidate%in%globs$targs) {
globs$targs=c(globs$targs,candidate)
globs$posits=c(globs$posits,1)
}else{
globs$targ=which(globs$targs==candidate)
globs$pnew=globs$posits[globs$targ]
globs$posits[globs$targ]=(globs$pnew%%4)+1
}
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}
if(length(globs$selx)>0) drawSel(globs$selx,globs$sely)
}else{
globs$selx=c(globs$selx,globs$xf)
globs$sely=c(globs$sely,globs$yf)
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}
drawSel(globs$selx,globs$sely)
}
}
}
if(1%in%buttons) {
# Delete the last gene which was highlighted
globs$targs=globs$targs[-length(globs$targs)]
globs$posits=globs$posits[-length(globs$posits)]
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}
}
if(2%in%buttons) {
# Open gene webpage on SGD
globs$xf=grconvertX(x,from="ndc",to="user")
globs$yf=grconvertY(y,from="ndc",to="user")
candidate=targFun(globs$xf,globs$yf,globs$dat)
directurl="http://www.this-page-intentionally-left-blank.org/"
if(!is.na(pmatch("Y",globs$dat$ORF[candidate]))) directurl=paste("http://www.yeastgenome.org/locus/",globs$dat$ORF[candidate],sep="")
if(!is.na(pmatch("SP",globs$dat$ORF[candidate]))) directurl=paste("http://www.pombase.org/spombe/result/",globs$dat$ORF[candidate],sep="")
browseURL(directurl)
}
}
keybd=function(key){
key=tolower(key)
if(key=="b") {
# Print data to console
cat("\nExperimental metadata: plot",globs$datno,"\n~~~~~~~~~~~~~~~\n")
# Split report string and patch in replicate numbers for Query and Control
rept=globs$datlist[[globs$datno]]$rept
fcont=grep("Control",rept)
if (length(fcont)==0) fcont=grep("x-axis",rept)
findx=tail(fcont,1)
rept2=c(rept[1:findx],paste("x-axis number of replicates:",globs$datlist[[globs$datno]]$cRep),rept[(findx+1):length(rept)],paste("y-axis number of replicates:",globs$datlist[[globs$datno]]$qRep))
cat(rept2,sep="\n")
}
if(key=="c") {
# Clear highlighted/selected points
globs$targs=c()
globs$posits=c()
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}
}
if(key=="d"){
# Unhighlight the last gene which was highlighted
globs$targs=globs$targs[-length(globs$targs)]
globs$posits=globs$posits[-length(globs$posits)]
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}
}
if(key=="i") {
# Change index for ratio plot
globs$indNo=globs$indNo+1
globs$ind=globs$indPoss[globs$indNo%%length(globs$indPoss)+1]
if(globs$rankPlot){rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)}
}
if(key=="k"){
# Change value plotted on y-axis in ratio plot
globs$ratplotIndNo=globs$ratplotIndNo+1
globs$ratploty=globs$ratplotyPoss[globs$ratplotIndNo%%length(globs$ratplotyPoss)+1]
if(globs$rankPlot){rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)}
}
if(key=="l") {
# Log ratio plot
globs$rankPlot=!globs$rankPlot
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}
}
if(key=="m") {
pdfname=sprintf("QFAVisualisation%04d.pdf",globs$plotno)
cat("Printing plot to file:",file.path(getwd(),pdfname),"\n")
pdf(pdfname)
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol,focusPlot=FALSE)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol,focusPlot=FALSE)
}
dev.off()
globs$plotno=globs$plotno+1
if ((Sys.info()['sysname']=="Windows")) bringToTop()
}
if(key=="n") {
pngname=sprintf("QFAVisualisation%04d.png",globs$plotno)
cat("Printing plot to file:",file.path(getwd(),pngname),"\n")
png(pngname,width=480*2.5,height=480*2.5,pointsize=12*2)
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol,focusPlot=FALSE)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol,focusPlot=FALSE)
}
dev.off()
globs$plotno=globs$plotno+1
if ((Sys.info()['sysname']=="Windows")) bringToTop()
}
if(key=="p") {
psname=sprintf("QFAVisualisation%04d.ps",globs$plotno)
cat("Printing plot to file:",file.path(getwd(),psname),"\n")
cairo_ps(psname)
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol,focusPlot=FALSE)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol,focusPlot=FALSE)
}
dev.off()
globs$plotno=globs$plotno+1
if ((Sys.info()['sysname']=="Windows")) bringToTop()
}
if(key=="q") return(invisible(1))
if(key=="r") {
# Zoom mode (click on TL and BR)
globs$zooming=TRUE
globs$zoomTL=c(-99,-99)
globs$zoomBR=c(-99,-99)
}
if((key=="s")&(length(globs$selx)>0)){
# Highlight genes encircled with select tool
if(globs$rankPlot){
ptsind=point.in.polygon(globs$dat[[globs$ind]],globs$dat[[globs$ratploty]],globs$selx,globs$sely)
}else{
ptsind=point.in.polygon(globs$dat$ControlFitnessSummary,globs$dat$QueryFitnessSummary,globs$selx,globs$sely)
}
globs$tsel=which(ptsind==1)
globs$targs=c(globs$targs,globs$tsel)
globs$posits=c(globs$posits,rep(1,length(globs$tsel)))
globs$selx=c()
globs$sely=c()
globs$sel=0
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}
}
if(key=="t") {
globs$ColourScheme=(globs$ColourScheme+1)%%3
# Toggle suppressor and enhancer colours
if(globs$ColourScheme==0){
globs$Ecol=rgb(0.4,0.4,1)
globs$Scol=rgb(1,0.4,0.4)
globs$ESymbol=25
globs$SSymbol=24
}
if(globs$ColourScheme==1){
globs$Ecol=rgb(1,0.4,0.4)
globs$Scol=rgb(0.4,0.4,1)
globs$ESymbol=25
globs$SSymbol=24
}
if(globs$ColourScheme==2){
globs$Ecol="grey"
globs$Scol="grey"
globs$ESymbol=19
globs$SSymbol=19
}
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}
}
if(key=="u") {
# Get user input for a new list of genes
if (Sys.info()['sysname']=="Windows") bringToTop(which=-1)
newgrp=getText(globs$ORFGENE)
newdf=data.frame(Notes="Generated interactively by user",GroupName=newgrp[["Label"]],GroupID="VisTool")
newdf$GroupORFs=paste(newgrp[["ORFs"]],collapse=" ")
globs$GROUPS=rbind(globs$GROUPS,newdf)
globs$compno=length(globs$GROUPS$GroupORFs)
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}
}
if(key=="v"){
# Print selected genes to terminal and copy standard gene names to clipboard
printSelected(globs)
if(length(globs$targs)==0){
toClipboard("")
}else{
toClipboard(globs$dat$Gene[globs$targs])
}
}
if(key=="w"){
globs$targ=globs$targs[length(globs$targs)]
#browseURL(paste("http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=",globs$dat$ORF[globs$targ],sep=""))
directurl="http://www.this-page-intentionally-left-blank.org/"
if(!is.na(pmatch("Y",globs$dat$ORF[globs$targ]))) directurl=paste("http://www.yeastgenome.org/locus/",globs$dat$ORF[globs$targ],sep="")
if(!is.na(pmatch("SP",globs$dat$ORF[globs$targ]))) directurl=paste("http://www.pombase.org/spombe/result/",globs$dat$ORF[globs$targ],sep="")
browseURL(directurl)
}
if(key=="x"){
# Print selected genes to terminal and copy systematic gene names to clipboard
printSelected(globs)
if(length(globs$targs)==0){
toClipboard("")
}else{
toClipboard(globs$dat$ORF[globs$targs])
}
}
if(key=="z") {
if(globs$sel==0){
globs$selx=c()
globs$sely=c()
}
globs$sel=(globs$sel+1)%%3
if(globs$sel==2){
# Close polygon
globs$selx=c(globs$selx,globs$selx[1])
globs$sely=c(globs$sely,globs$sely[1])
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}
drawSel(globs$selx,globs$sely)
globs$sel=0
}
}
if(key=="right") {
globs$datno<<-(globs$datno%%length(globs$datlist))+1
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}
globs$orftargs=globs$dat$ORF[globs$targs]
globs$dat=globs$datlist[[globs$datno]]$res
globs$targs=match(globs$orftargs,globs$dat$ORF)
}
if(key=="left") {
globs$datno=((globs$datno-2)%%length(globs$datlist))+1
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}
orftargs=globs$dat$ORF[globs$targs]
globs$dat=globs$datlist[[globs$datno]]$res
globs$targs=match(globs$orftargs,globs$dat$ORF)
}
if(key=="up") {
globs$compno=(globs$compno+1)%%(length(globs$GROUPS$GroupORFs)+1)
#if(globs$compno>length(globs$GROUPS$GroupORFs)) globs$compno=1
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}
}
if(key=="down") {
globs$compno=(globs$compno-1)%%(length(globs$GROUPS$GroupORFs)+1)
#if(globs$compno<=0) globs$compno=length(globs$GROUPS$GroupORFs)
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}
}
return(NULL)
}
visTool<-function(groups,orf2gene,GISfiles,metaRep="MetaReport.txt",fitmax=0,reg="lmreg"){
# Function for generating interactive plot
globs$GROUPS=groups()
globs$ORFGENE=orf2gene
globs$datlist=list()
globs$reg=reg
clients=c()
dates=c()
for (f in 1:length(GISfiles)){
report=getResults(GISfiles[f])
report$res$ratio=pmax(0.005,report$res$QueryFitnessSummary/report$res$ControlFitnessSummary)
report$res$gindex=rank(as.character(report$res$Gene))
report$res$oindex=rank(as.character(report$res$ORF))
report$res$cindex=rank(report$res$ControlFitnessSummary)
report$res$qindex=rank(report$res$QueryFitnessSummary)
report$res$rindex=rank(report$res$QueryFitnessSummary/report$res$ControlFitnessSummary)
#report$datname=paste("Plot",paste(f,":",sep=""),report$summType,"fitness",paste("(",report$testType,")",sep=""))
globs$datlist[[f]]=report
clients=c(clients,report$qCli)
dates=c(dates,report$qDate)
}
# Re-order plots by query client and then by query date
# Takes 22s for 138 datasets...
dlist=unlist(globs$datlist)
dlist=dlist[order(clients,dates)]
dlist=as.list(dlist)
neworder=order(clients,dates)
newDatList=list()
for (i in 1:length(neworder)){
newDatList[[i]]=globs$datlist[[neworder[i]]]
newDatList[[i]]$datname=paste("Plot",paste(i,":",sep=""),newDatList[[i]]$summType,"fitness",paste("(",newDatList[[i]]$testType,")",sep=""))
}
globs$datlist=newDatList
reportExpts(globs,fname=metaRep)
globs$fxmax=c();globs$fymax=c()
globs$fxmin=c();globs$fymin=c()
for(d in globs$datlist){
if(fitmax==0){
globs$fxmax=c(globs$fxmax,d$fMax)
globs$fymax=c(globs$fymax,d$fMax)
}else{
globs$fxmax=c(globs$fxmax,fitmax)
globs$fymax=c(globs$fymax,fitmax)
}
globs$fxmin=c(0,globs$fxmin)
globs$fymin=c(0,globs$fymin)
}
globs$n=0
globs$targs=c()
globs$posits=c()
globs$sel=0
globs$selx=c()
globs$sely=c()
globs$indPoss=c("gindex","oindex","rindex","cindex","qindex")
globs$indNo=0
globs$ind=globs$indPoss[globs$indNo%%length(globs$indPoss)+1]
# Toggling between colour of suppressors and enhancers
globs$ColourScheme=0
globs$Ecol=rgb(0.4,0.4,1)
globs$Scol=rgb(1,0.4,0.4)
globs$ESymbol=25
globs$SSymbol=24
cat("\nControls: Windows mouse\n")
cat("~~~~~~~~~~~~~~~\n")
cat("Left click: Highlight gene/Rotate text position\n")
cat("Right click: Open SGD page for gene (alternatively, press 'w' on keyboard)\n")
cat("Middle click: Remove last gene (alternatively, press 'd' on keyboard)\n\n")
cat("Controls: Mac mouse\n")
cat("~~~~~~~~~~~~~~~\n")
cat("Click: Highlight gene/Rotate text position\n\n")
cat("Controls: Keyboard\n")
cat("~~~~~~~~~~~~~~~\n")
cat("Left/Right arrow: Switch to next/previous fitness plot (comparison between different pair of experiments).\n")
cat("Up/Down arrow: Change group of genes currently highlighted (in purple).\n")
cat("b: Print experimental metadata report to console window\n")
cat("c: Clear highlighting from currently selected genes.\n")
cat("d: Remove highlighting from last gene highlighted.\n")
cat("i: In rank plot mode, toggle between x-axis rank order.\n")
cat("k: In rank plot mode, toggle between fitness ratio, GIS, query fitness and control fitness on y-axis.\n")
cat("l: Toggle plot style between fitness plot (default) and rank plot mode.\n")
cat("p: Save current plot as vector graphic to QFAVisualisation.ps. Other filetypes can also be generated - 'n': .png and 'm': .pdf\n")
cat("q: Quit tool and print gene names currently selected to console window.\n")
cat("r: Enter zoom mode. Click on top left and bottom right of area to inspect (experimental, may have to quit to zoom out...).\n")
cat("s: Highlight genes encircled using select tool ('z').\n")
cat("t: Toggle between colours (blue/red) highlighting positive/negative interactions, and no highlighting.\n")
cat("u: Add new group of genes to list of highlightable groups.\n")
cat("v: Print list of currently selected genes to console and copy standard gene names to clipboard\n")
cat("w: Open SGD web-page for last gene highlighted.\n")
cat("x: Print list of currently selected genes to console and copy systematic gene names to clipboard\n")
cat("z: Toggle select tool on/off. Select genes for highlighting by drawing a polygon on plot. Press 's' to add selection when finished.\n")
globs$datno=1
globs$plotno=1
globs$compno=0
globs$pos=1
globs$zooming=FALSE
globs$zoomTL=c(-99,-99)
globs$zoomBR=c(-99,-99)
globs$rankPlot=FALSE
globs$ratplotyPoss=c("ratio","GIS","QueryFitnessSummary","QueryFitnessSummaryLOG","ControlFitnessSummary","ControlFitnessSummaryLOG")
globs$ratplotIndNo=0
globs$ratploty=globs$ratplotyPoss[globs$ratplotIndNo%%length(globs$ratplotyPoss)+1]
globs$dat=globs$datlist[[globs$datno]]$res
# Check if running under windows, if not, force X11
# Note that event handling doesn't work under Linux :(
sysinf=Sys.info()
#if( sysinf["sysname"]!="Windows") x11()
#if( sysinf["sysname"]=="Linux") Cairo()
x11()
#dev.new()
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}
getGraphicsEvent(prompt="Left/Right: Change plot, b: Expt. metadata, L-click: Highlight, M-click: Remove, q: quit", onMouseDown=mouse, onKeybd=keybd)
printSelected(globs)
#if( sysinf["sysname"]!="Windows") dev.off()
dev.off()
}
return(visTool)
}
complexesFromSource<-function(){
# Read in functionally related complexes
# Largely from Benschopp Mol Cell 2010
# Can add some complexes manually
compfile=file.path(system.file(package = "qfa"),"extdata","FunctionalComplexes.txt",sep="")
Complexes=read.delim(compfile,stringsAsFactors=FALSE,sep="\t")
Complexes$CompList=gsub(";"," ",gsub("\\s","",Complexes$Complex.members..systematic.name))
res=data.frame(GroupName=Complexes$X..Complex.name,GroupID="Func.")
res$GroupORFs=Complexes$CompList
return(res)
}
buildComplexes<-function(){
fname=file.path(system.file(package = "qfa"),"extdata","FunctionalComplexes.txt")
cat("\nGroups of functionally related complexes are specified a tab-delimited text file\n which can be found at the path below. This file can be edited with any text editor. Please note that under OSX, this path might be hidden. You can still find and edit the file by copying the path below, opening Finder->Go->Go to File and pasting into the dialogue box.\n")
cat(paste(fname,"\n"))
ComplexesData=read.delim(fname,sep="\t",header=TRUE,stringsAsFactors=FALSE)
return(ComplexesData)
}
buildBenschop<-function() buildComplexes()
iRVisDemo<-function(groupFun=buildComplexes,fitmax=0,reg="lmreg"){
orfile=file.path(file.path(system.file(package = "qfa"),"extdata","ORF2GENE.txt"))
ORFGENE=read.delim(orfile,stringsAsFactors=FALSE,sep="\t",header=FALSE)
colnames(ORFGENE)=c("ORF","Gene")
ORFGENE=ORFGENE[!duplicated(ORFGENE$ORF),]
# Read in GIS files
filenames=list.files(file.path(system.file(package = "qfa"),"extdata"),pattern="\\GIS.txt$",full.names=TRUE)
visTool=makeVisTool()
visTool(groupFun,ORFGENE,filenames,"MetaReport.txt",fitmax=fitmax,reg=reg)
}
NAtoBlank=function(x){
return(ifelse((is.na(x))|(x=="NA"),"",x))
}
getResults<-function(filename){
#print(filename)
# Need to detect at least two different kinds of header now...
fopen=file(filename,"rt")
i=1
while(!grepl("############",readLines(fopen,1))) i=i+1
close(fopen)
cStart=-1 # At what line does control metadata start?
qStart=-1 # At what line does query metadata start?
res=read.delim(filename,skip=i,header=TRUE,stringsAsFactors=FALSE)
hdr=read.delim(filename,nrows=i-1,header=FALSE,stringsAsFactors=FALSE)$V1
for(hdrow in 1:length(hdr)){
if(((grepl("x-axis ",hdr[hdrow]))||(grepl("Control ",hdr[hdrow])))&&(cStart<0)) cStart=hdrow
if(((grepl("y-axis ",hdr[hdrow]))||(grepl("Query ",hdr[hdrow])))&&(qStart<0)) qStart=hdrow
}
qfaVersion=NAtoBlank(strsplit(hdr[1],": ")[[1]][2])
summType=NAtoBlank(strsplit(hdr[2],": ")[[1]][2])
testType=NAtoBlank(strsplit(hdr[3],": ")[[1]][2])
cTreat=NAtoBlank(strsplit(hdr[cStart+0],": ")[[1]][2])
cMed=NAtoBlank(strsplit(hdr[cStart+1],": ")[[1]][2])
cScrID=NAtoBlank(strsplit(hdr[cStart+2],": ")[[1]][2])
cScrNm=NAtoBlank(strsplit(hdr[cStart+3],": ")[[1]][2])
cLibs=NAtoBlank(strsplit(hdr[cStart+4],": ")[[1]][2])
cCli=NAtoBlank(strsplit(hdr[cStart+5],": ")[[1]][2])
cUse=NAtoBlank(strsplit(hdr[cStart+6],": ")[[1]][2])
cDate=NAtoBlank(strsplit(hdr[cStart+7],": ")[[1]][2])
cDate=gsub("'","",cDate)
cDate=gsub('"',"",cDate)
cPI=cCond=cInoc=cFit=""
if(cStart+8<qStart) cPI=NAtoBlank(strsplit(hdr[cStart+8],": ")[[1]][2])
if(cStart+9<qStart) cCond=NAtoBlank(strsplit(hdr[cStart+9],": ")[[1]][2])
if(cStart+10<qStart) cInoc=NAtoBlank(strsplit(hdr[cStart+10],": ")[[1]][2])
if(cStart+11<qStart) cFit=NAtoBlank(strsplit(hdr[cStart+11],": ")[[1]][2])
qTreat=NAtoBlank(strsplit(hdr[qStart+0],": ")[[1]][2])
qMed=NAtoBlank(strsplit(hdr[qStart+1],": ")[[1]][2])
qScrID=NAtoBlank(strsplit(hdr[qStart+2],": ")[[1]][2])
qScrNm=NAtoBlank(strsplit(hdr[qStart+3],": ")[[1]][2])
qLibs=NAtoBlank(strsplit(hdr[qStart+4],": ")[[1]][2])
qCli=NAtoBlank(strsplit(hdr[qStart+5],": ")[[1]][2])
qUse=NAtoBlank(strsplit(hdr[qStart+6],": ")[[1]][2])
qDate=NAtoBlank(strsplit(hdr[qStart+7],": ")[[1]][2])
qDate=gsub("'","",qDate)
qDate=gsub('"',"",qDate)
qPI=qCond=qInoc=qFit=""
if(qStart+8<=length(hdr)) qPI=NAtoBlank(strsplit(hdr[qStart+8],": ")[[1]][2])
if(qStart+9<=length(hdr)) qCond=NAtoBlank(strsplit(hdr[qStart+9],": ")[[1]][2])
if(qStart+10<=length(hdr)) qInoc=NAtoBlank(strsplit(hdr[qStart+10],": ")[[1]][2])
if(qStart+11<=length(hdr)) qFit=NAtoBlank(strsplit(hdr[qStart+11],": ")[[1]][2])
fMax=max(c(res$QueryFitnessSummary,res$ControlFitnessSummary))
qRep=getMode(res$QueryCount)
cRep=getMode(res$ControlCount)
return(
list(res=res,qfaVersion=qfaVersion,summType=summType,testType=testType,
cTreat=cTreat,cMed=cMed,cScrID=cScrID,cScrNm=cScrNm,cLibs=cLibs,cCli=cCli,cUse=cUse,cDate=cDate,cPI=cPI,cCond=cCond,cInoc=cInoc,cFit=cFit,
qTreat=qTreat,qMed=qMed,qScrID=qScrID,qScrNm=qScrNm,qLibs=qLibs,qCli=qCli,qUse=qUse,qDate=qDate,qPI=qPI,qCond=qCond,qInoc=qInoc,qFit=qFit,
fMax=fMax,rept=hdr,qRep=qRep,cRep=cRep)
)
}
toClipboard=function(x,sep="\n"){
# Platform-independent paste-to-clipboard function
x=as.character(x)
if(Sys.info()["sysname"]=="Windows"){
writeClipboard(x)
}else{
osxclipboard <- pipe("pbcopy","w")
write(x,file=osxclipboard,sep=sep)
close(osxclipboard)
}
}
buildGO<-function(){
# Note we do not recommend that users edit this particular set of functionally related genes
fname=file.path(system.file(package = "qfa"),"extdata","GOAnnotation.txt")
cat("\nGrouping of genes by GO terms specified in this text file\n~~~~~~~~~~~~~~~\n")
cat(paste(fname,"\n"))
GO=read.delim(fname,sep="\t",header=TRUE,stringsAsFactors=FALSE)
return(GO)
}
buildPombeGO<-function(){
# Note we do not recommend that users edit this particular set of functionally related genes
fname=file.path(system.file(package = "qfa"),"extdata","pombeGOAnnotation.txt")
cat("\nGrouping of genes by GO terms specified in this text file:\n~~~~~~~~~~~~~~~\n")
cat(paste(fname,"\n"))
GO=read.delim(fname,sep="\t",header=TRUE,stringsAsFactors=FALSE)
return(GO)
}
getText=function(ORFGENE){
x=list()
cat("Input a list of gene names, separated by spaces & press enter:\n")
usergenes=scan(what=character(),nlines=1)
usergenes=toupper(usergenes)
cat("Please input a label for your list of genes (no spaces) & press enter:\n")
lab=scan(what=character(),nlines=1,n=1)
orfs=c()
genes=c()
for(gene in usergenes){
if (gene%in%toupper(ORFGENE$ORF)) {
orfs=c(orfs,gene)
genes=c(genes,ORFGENE$Gene[toupper(ORFGENE$ORF)==gene])
} else {
if(gene%in%toupper(ORFGENE$Gene)){
# Standard gene names are ambiguous
# In this scenario, they do not unambiguously specify species (e.g. RIF1 in cerevisiae and pombe)
orfs=c(orfs,ORFGENE$ORF[toupper(ORFGENE$Gene)==gene])
genes=c(genes,gene)
}
}
}
x[["Genes"]]=genes
x[["ORFs"]]=orfs
x[["Label"]]=lab
print(x)
return(x)
}
drawSel=function(selx,sely){
if(length(selx)==1) {
points(selx,sely,col="black",pch=16,cex=0.4)
}else{
points(selx,sely,col="black",lty=2,type="l")
}
}
printSelected=function(globs){
cat("~~~~~~~~~~~~~~~\n")
cat("\n")
cat("List of genes currently selected:\n")
cat(globs$dat$Gene[globs$targs])
cat("\n")
cat("~~~~~~~~~~~~~~~\n")
cat("\n")
cat("Systematic names for genes currently selected:\n")
cat(globs$dat$ORF[globs$targs])
cat("\n")
cat("\n")
cat("\n")
}
reportExpts=function(globs,fname="MetaReport.txt"){
if(fname!="") {
cat("\nDetailed plot metadata will be written to file:\n")
cat(file.path(getwd(),fname),"\n")
sink(fname)
}
metaSumm=data.frame(PlotNo=numeric(),x.axis=character(),y.axis=character(),stringsAsFactors=FALSE)
for (datno in 1:length(globs$datlist)){
metaSumm[datno,]=c(datno,paste(globs$datlist[[datno]]$cScrNm,globs$datlist[[datno]]$cTreat,globs$datlist[[datno]]$cCond,globs$datlist[[datno]]$cFit),paste(globs$datlist[[datno]]$qScrNm,globs$datlist[[datno]]$qTreat,globs$datlist[[datno]]$qCond,globs$datlist[[datno]]$qFit))
# Print data to console
cat("\nExperimental metadata: plot",datno,"\n")
# Split report string and patch in replicate numbers for Query and Control
rept=globs$datlist[[datno]]$rept
fcont=grep("Control",rept)
if (length(fcont)==0) fcont=grep("x-axis",rept)
findx=tail(fcont,1)
rept2=c(rept[1:findx],paste("x-axis number of replicates:",globs$datlist[[datno]]$cRep),rept[(findx+1):length(rept)],paste("y-axis number of replicates:",globs$datlist[[datno]]$qRep))
strt=4
r2=rept2[strt:length(rept2)]
fin=length(r2)
reptCont=r2[1:(fin/2)]
reptCont=gsub("Control ","",reptCont)
reptQuer=r2[((fin/2)+1):fin]
reptQuer=gsub("Query ","",reptQuer)
df=data.frame(Control=reptCont,Query=reptQuer)
#print(df,row.names=FALSE)
cat(rept2,sep="\n")
}
if(fname!="") sink()
flist=strsplit(fname,"\\.")[[1]]
froot=head(flist,1)
fext=tail(flist,1)
froot2=paste(froot,"Summary",sep="")
fname2=paste(froot2,fext,sep=".")
cat("\nExperimental metadata summary written to file:\n")
cat(file.path(getwd(),fname2),"\n")
cat("\nExperimental metadata summary:\n")
print(metaSumm,row.names=FALSE)
write.table(metaSumm,file=fname2,sep="\t",row.names=FALSE,quote=FALSE)
}
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Defines functions makeVisTool complexesFromSource buildComplexes buildBenschop iRVisDemo NAtoBlank getResults toClipboard buildGO buildPombeGO getText drawSel printSelected reportExpts
Documented in buildBenschop buildComplexes buildGO buildPombeGO complexesFromSource drawSel getResults getText iRVisDemo makeVisTool NAtoBlank printSelected reportExpts toClipboard
# Huge function closure to keep visualisation tool environment out of global environment and keep CRAN happy
makeVisTool=function(){
globs<-new.env()
# Plotting function
epiplot<-function(results,qthresh,fitratio=FALSE,ref.orf="YOR202W",xxlab="Control Fitness",yylab="Query Fitness",mmain="Epistasis Plot",ymin=0,ymax=0,xmin=0,xmax=0,ecol="green",scol="red",esym=19,ssym=19,reg="lmreg"){
enhancers<-gethits(results,qthresh,type="E")
suppressors<-gethits(results,qthresh,type="S")
others<-results[(!results$ORF%in%enhancers$ORF)&(!results$ORF%in%suppressors$ORF),]
plot(NULL,type="n",xlim=c(xmin,xmax),ylim=c(ymin,ymax),
xlab=xxlab,ylab=yylab,main=mmain,
col=8,pch=19,cex=0.5)
# Add line for genetic independence
if (fitratio!=FALSE){abline(0,fitratio,lwd=2,col=8)} else {
slp=lm.epi(results$QueryFitnessSummary,results$ControlFitnessSummary,modcheck=FALSE,reg="lmreg")
abline(0,slp,lwd=2,col=8)}
# Add 1:1 fitness line
abline(0,1,lwd=2,lty=4,col=8)
# Add reference ORF fitnesses lines
if (ref.orf!=FALSE){
reforf<-results[results$ORF==ref.orf,]
abline(v=reforf$ControlFitnessSummary,col="lightblue",lwd=2)
abline(h=reforf$QueryFitnessSummary,col="lightblue",lwd=2)}
# Add points for non-suppressors & non-enhancers
points(others$ControlFitnessSummary,others$QueryFitnessSummary,col="grey",cex=0.75,pch=19)
#text(others$ControlFitnessSummary,others$QueryFitnessSummary,others$Gene,col="grey",pos=4,offset=0.1,cex=0.4)
# Add suppressors & enhancers
if(length(enhancers$ORF)>0){
points(enhancers$ControlFitnessSummary,enhancers$QueryFitnessSummary,col=ecol,bg=ecol,pch=esym,cex=0.75)
#text(enhancers$ControlFitnessSummary,enhancers$QueryFitnessSummary,enhancers$Gene,col=1,pos=4,offset=0.1,cex=0.4)
}
if(length(suppressors$ORF)>0){
points(suppressors$ControlFitnessSummary,suppressors$QueryFitnessSummary,col=scol,bg=scol,pch=ssym,cex=0.75)
#text(suppressors$ControlFitnessSummary,suppressors$QueryFitnessSummary,suppressors$Gene,col=1,pos=4,offset=0.1,cex=0.4)
}
}
makePlot=function(datno,focusPlot=TRUE,...){
if(globs$compno>0){
lst=strsplit(globs$GROUPS$GroupORFs[globs$compno]," ")[[1]]
Ngrp=paste("(N=",length(lst),")",sep="")
compnm=paste("Group",paste(globs$compno,":",sep=""),globs$GROUPS$GroupName[globs$compno],Ngrp,globs$GROUPS$GroupID[globs$compno])
}else{
compnm=""
}
#plotdesc=paste(globs$datlist[[datno]]$datname,globs$datlist[[datno]]$cScrNm,globs$datlist[[datno]]$cTreat,":",globs$datlist[[datno]]$qScrNm,globs$datlist[[datno]]$qTreat)
plotdesc=globs$datlist[[datno]]$datname
maintitle=paste(plotdesc,compnm,sep="\n")
if (globs$datlist[[datno]]$cCond=="") {ControlCondition=globs$datlist[[datno]]$cMed}else{ControlCondition=globs$datlist[[datno]]$cCond}
if (globs$datlist[[datno]]$qCond=="") {QueryCondition=globs$datlist[[datno]]$qMed}else{QueryCondition=globs$datlist[[datno]]$qCond}
xlab=paste(globs$datlist[[datno]]$cScrNm,globs$datlist[[datno]]$cTreat,ControlCondition,globs$datlist[[datno]]$cFit,globs$datlist[[datno]]$cInoc,globs$datlist[[datno]]$cScrID,globs$datlist[[datno]]$cCli,globs$datlist[[datno]]$cDate)
ylab=paste(globs$datlist[[datno]]$qScrNm,globs$datlist[[datno]]$qTreat,QueryCondition,globs$datlist[[datno]]$qFit,globs$datlist[[datno]]$qInoc,globs$datlist[[datno]]$qScrID,globs$datlist[[datno]]$qCli,globs$datlist[[datno]]$qDate)
globs$orftargs=globs$dat$ORF[globs$targs]
globs$dat=globs$datlist[[datno]]$res
globs$targs=match(toupper(globs$orftargs),toupper(globs$dat$ORF))
epiplot(globs$dat,0.05,mmain=maintitle,xxlab=xlab,yylab=ylab,ymin=globs$fymin[datno],ymax=globs$fymax[datno],xmin=globs$fxmin[datno],xmax=globs$fxmax[datno],reg=globs$reg,...)
if(globs$compno>0){
lst=strsplit(globs$GROUPS$GroupORFs[globs$compno]," ")[[1]]
dcomp=globs$dat[toupper(globs$dat$ORF)%in%toupper(lst),]
if(length(dcomp$ORF)>0){
points(dcomp$ControlFitnessSummary,dcomp$QueryFitnessSummary,col="purple",pch=16,cex=1.5)
text(dcomp$ControlFitnessSummary,dcomp$QueryFitnessSummary,dcomp$Gene,pos=sample(1:4,length(dcomp$Gene),replace=TRUE),cex=1.0)
}
}
if(length(globs$targs)>0){
points(globs$dat$ControlFitnessSummary[globs$targs],globs$dat$QueryFitnessSummary[globs$targs],col="blue",pch=16,cex=0.2)
text(globs$dat$ControlFitnessSummary[globs$targs],globs$dat$QueryFitnessSummary[globs$targs],globs$dat$Gene[globs$targs],pos=globs$posits,cex=0.75)
}
if ((Sys.info()['sysname']=="Windows")&focusPlot) bringToTop()
}
rnkPlot=function(datno,focusPlot=TRUE,qthresh=0.05,ecol="green",scol="red",esym=19,ssym=19){
if(globs$compno>0){
lst=strsplit(globs$GROUPS$GroupORFs[globs$compno]," ")[[1]]
Ngrp=paste("(N=",length(lst),")",sep="")
compnm=paste("Group",paste(globs$compno,":",sep=""),globs$GROUPS$GroupName[globs$compno],Ngrp,globs$GROUPS$GroupID[globs$compno])
}else{
compnm=""
}
maintitle=paste(globs$datlist[[datno]]$datname,compnm,sep="\n")
xlab=paste(globs$datlist[[datno]]$cScrID)
ylab=paste(globs$datlist[[datno]]$qScrID)
if(globs$ratploty=="ratio") {axislab=paste("Fit ",ylab,"/Fit ",xlab," (log scale)",sep=""); ratlog="y"}
if(globs$ratploty=="GIS") {axislab=paste("GIS ",ylab," vs. ",xlab," (linear scale)",sep=""); ratlog=""}
if(globs$ratploty=="QueryFitnessSummary") {axislab=paste("Query Fit ",ylab," (linear scale)",sep=""); ratlog=""}
if(globs$ratploty=="ControlFitnessSummary") {axislab=paste("Control Fit ",xlab," (linear scale)",sep=""); ratlog=""}
if(globs$ratploty=="QueryFitnessSummaryLOG") {axislab=paste("Query Fit ",ylab," (log scale)",sep=""); ratlog="y"}
if(globs$ratploty=="ControlFitnessSummaryLOG") {axislab=paste("Control Fit ",xlab," (log scale)",sep=""); ratlog="y"}
globs$orftargs=globs$dat$ORF[globs$targs]
if(globs$ind=="gindex") ratlab="Ranked by standard gene name (alphabetical order)"
if(globs$ind=="oindex") ratlab="Ranked by systematic gene name (chromosome coordinate)"
if(globs$ind=="cindex") ratlab="Ranked by control fitness"
if(globs$ind=="qindex") ratlab="Ranked by query fitness"
if(globs$ind=="rindex") ratlab="Ranked by query/control fitness ratio"
globs$dat=globs$datlist[[datno]]$res
globs$targs=match(globs$orftargs,globs$dat$ORF)
rply=gsub("LOG","",globs$ratploty)
plot(globs$dat[[globs$ind]],globs$dat[[rply]],xlab=ratlab,log=ratlog,ylab=axislab,main=maintitle,col="grey",cex=0.5,pch=19)
if(globs$compno>0){
lst=strsplit(globs$GROUPS$GroupORFs[globs$compno]," ")[[1]]
globs$dcomp=globs$dat[globs$dat$ORF%in%lst,]
if(length(globs$dcomp$ORF)>0){
points(globs$dcomp[[globs$ind]],globs$dcomp[[rply]],col="purple",pch=16,cex=1.5)
text(globs$dcomp[[globs$ind]],globs$dcomp[[rply]],globs$dcomp$Gene,pos=1,cex=1.0)
}
}
if(length(globs$targs)>0){
points(globs$dat[[globs$ind]][globs$targs],globs$dat[[rply]][globs$targs],col="blue",pch=16,cex=0.2)
text(globs$dat[[globs$ind]][globs$targs],globs$dat[[rply]][globs$targs],globs$dat$Gene[globs$targs],pos=globs$posits,cex=0.75)
}
if ((Sys.info()['sysname']=="Windows")&focusPlot) bringToTop()
}
targFun=function(x,y,datobj){
if(globs$rankPlot){
rply=gsub("LOG","",globs$ratploty)
if(globs$ratploty=="ratio"){
d=((x-datobj[[globs$ind]])/max(datobj[[globs$ind]]))^2+(y-datobj[[rply]])^2
}else{
d=(x/max(datobj[[globs$ind]])-datobj[[globs$ind]]/max(datobj[[globs$ind]]))^2+(y/max(datobj[[rply]])-datobj[[rply]]/max(datobj[[rply]]))^2
}
}else{
d=(x-datobj$ControlFitnessSummary)^2+(y-datobj$QueryFitnessSummary)^2
}
best=which.min(d)
return(best)
}
mouse=function(buttons,x,y){
if(0%in%buttons) {
# Problem with Cairo coordinate system here...
globs$xf=grconvertX(x,from="ndc",to="user")
globs$yf=grconvertY(y,from="ndc",to="user")
if(globs$zooming==TRUE){
if(identical(globs$zoomTL,c(-99,-99))) {
globs$zoomTL=c(globs$xf,globs$yf)
}else{
globs$zoomBR=c(globs$xf,globs$yf)
# Zoom in!
globs$fxmin[globs$datno]=globs$zoomTL[1]
globs$fxmax[globs$datno]=globs$zoomBR[1]
globs$fymin[globs$datno]=globs$zoomBR[2]
globs$fymax[globs$datno]=globs$zoomTL[2]
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}
# Reset zooming parameters
globs$zooming=FALSE
globs$zoomTL=c(-99,-99)
globs$zoomBR=c(-99,-99)
}
}else{
if(globs$sel==0){
# Find nearest gene, highlight location, draw plot
candidate=targFun(globs$xf,globs$yf,globs$dat)
if(!candidate%in%globs$targs) {
globs$targs=c(globs$targs,candidate)
globs$posits=c(globs$posits,1)
}else{
globs$targ=which(globs$targs==candidate)
globs$pnew=globs$posits[globs$targ]
globs$posits[globs$targ]=(globs$pnew%%4)+1
}
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}
if(length(globs$selx)>0) drawSel(globs$selx,globs$sely)
}else{
globs$selx=c(globs$selx,globs$xf)
globs$sely=c(globs$sely,globs$yf)
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}
drawSel(globs$selx,globs$sely)
}
}
}
if(1%in%buttons) {
# Delete the last gene which was highlighted
globs$targs=globs$targs[-length(globs$targs)]
globs$posits=globs$posits[-length(globs$posits)]
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}
}
if(2%in%buttons) {
# Open gene webpage on SGD
globs$xf=grconvertX(x,from="ndc",to="user")
globs$yf=grconvertY(y,from="ndc",to="user")
candidate=targFun(globs$xf,globs$yf,globs$dat)
directurl="http://www.this-page-intentionally-left-blank.org/"
if(!is.na(pmatch("Y",globs$dat$ORF[candidate]))) directurl=paste("http://www.yeastgenome.org/locus/",globs$dat$ORF[candidate],sep="")
if(!is.na(pmatch("SP",globs$dat$ORF[candidate]))) directurl=paste("http://www.pombase.org/spombe/result/",globs$dat$ORF[candidate],sep="")
browseURL(directurl)
}
}
keybd=function(key){
key=tolower(key)
if(key=="b") {
# Print data to console
cat("\nExperimental metadata: plot",globs$datno,"\n~~~~~~~~~~~~~~~\n")
# Split report string and patch in replicate numbers for Query and Control
rept=globs$datlist[[globs$datno]]$rept
fcont=grep("Control",rept)
if (length(fcont)==0) fcont=grep("x-axis",rept)
findx=tail(fcont,1)
rept2=c(rept[1:findx],paste("x-axis number of replicates:",globs$datlist[[globs$datno]]$cRep),rept[(findx+1):length(rept)],paste("y-axis number of replicates:",globs$datlist[[globs$datno]]$qRep))
cat(rept2,sep="\n")
}
if(key=="c") {
# Clear highlighted/selected points
globs$targs=c()
globs$posits=c()
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}
}
if(key=="d"){
# Unhighlight the last gene which was highlighted
globs$targs=globs$targs[-length(globs$targs)]
globs$posits=globs$posits[-length(globs$posits)]
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}
}
if(key=="i") {
# Change index for ratio plot
globs$indNo=globs$indNo+1
globs$ind=globs$indPoss[globs$indNo%%length(globs$indPoss)+1]
if(globs$rankPlot){rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)}
}
if(key=="k"){
# Change value plotted on y-axis in ratio plot
globs$ratplotIndNo=globs$ratplotIndNo+1
globs$ratploty=globs$ratplotyPoss[globs$ratplotIndNo%%length(globs$ratplotyPoss)+1]
if(globs$rankPlot){rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)}
}
if(key=="l") {
# Log ratio plot
globs$rankPlot=!globs$rankPlot
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}
}
if(key=="m") {
pdfname=sprintf("QFAVisualisation%04d.pdf",globs$plotno)
cat("Printing plot to file:",file.path(getwd(),pdfname),"\n")
pdf(pdfname)
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol,focusPlot=FALSE)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol,focusPlot=FALSE)
}
dev.off()
globs$plotno=globs$plotno+1
if ((Sys.info()['sysname']=="Windows")) bringToTop()
}
if(key=="n") {
pngname=sprintf("QFAVisualisation%04d.png",globs$plotno)
cat("Printing plot to file:",file.path(getwd(),pngname),"\n")
png(pngname,width=480*2.5,height=480*2.5,pointsize=12*2)
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol,focusPlot=FALSE)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol,focusPlot=FALSE)
}
dev.off()
globs$plotno=globs$plotno+1
if ((Sys.info()['sysname']=="Windows")) bringToTop()
}
if(key=="p") {
psname=sprintf("QFAVisualisation%04d.ps",globs$plotno)
cat("Printing plot to file:",file.path(getwd(),psname),"\n")
cairo_ps(psname)
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol,focusPlot=FALSE)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol,focusPlot=FALSE)
}
dev.off()
globs$plotno=globs$plotno+1
if ((Sys.info()['sysname']=="Windows")) bringToTop()
}
if(key=="q") return(invisible(1))
if(key=="r") {
# Zoom mode (click on TL and BR)
globs$zooming=TRUE
globs$zoomTL=c(-99,-99)
globs$zoomBR=c(-99,-99)
}
if((key=="s")&(length(globs$selx)>0)){
# Highlight genes encircled with select tool
if(globs$rankPlot){
ptsind=point.in.polygon(globs$dat[[globs$ind]],globs$dat[[globs$ratploty]],globs$selx,globs$sely)
}else{
ptsind=point.in.polygon(globs$dat$ControlFitnessSummary,globs$dat$QueryFitnessSummary,globs$selx,globs$sely)
}
globs$tsel=which(ptsind==1)
globs$targs=c(globs$targs,globs$tsel)
globs$posits=c(globs$posits,rep(1,length(globs$tsel)))
globs$selx=c()
globs$sely=c()
globs$sel=0
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}
}
if(key=="t") {
globs$ColourScheme=(globs$ColourScheme+1)%%3
# Toggle suppressor and enhancer colours
if(globs$ColourScheme==0){
globs$Ecol=rgb(0.4,0.4,1)
globs$Scol=rgb(1,0.4,0.4)
globs$ESymbol=25
globs$SSymbol=24
}
if(globs$ColourScheme==1){
globs$Ecol=rgb(1,0.4,0.4)
globs$Scol=rgb(0.4,0.4,1)
globs$ESymbol=25
globs$SSymbol=24
}
if(globs$ColourScheme==2){
globs$Ecol="grey"
globs$Scol="grey"
globs$ESymbol=19
globs$SSymbol=19
}
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}
}
if(key=="u") {
# Get user input for a new list of genes
if (Sys.info()['sysname']=="Windows") bringToTop(which=-1)
newgrp=getText(globs$ORFGENE)
newdf=data.frame(Notes="Generated interactively by user",GroupName=newgrp[["Label"]],GroupID="VisTool")
newdf$GroupORFs=paste(newgrp[["ORFs"]],collapse=" ")
globs$GROUPS=rbind(globs$GROUPS,newdf)
globs$compno=length(globs$GROUPS$GroupORFs)
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}
}
if(key=="v"){
# Print selected genes to terminal and copy standard gene names to clipboard
printSelected(globs)
if(length(globs$targs)==0){
toClipboard("")
}else{
toClipboard(globs$dat$Gene[globs$targs])
}
}
if(key=="w"){
globs$targ=globs$targs[length(globs$targs)]
#browseURL(paste("http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=",globs$dat$ORF[globs$targ],sep=""))
directurl="http://www.this-page-intentionally-left-blank.org/"
if(!is.na(pmatch("Y",globs$dat$ORF[globs$targ]))) directurl=paste("http://www.yeastgenome.org/locus/",globs$dat$ORF[globs$targ],sep="")
if(!is.na(pmatch("SP",globs$dat$ORF[globs$targ]))) directurl=paste("http://www.pombase.org/spombe/result/",globs$dat$ORF[globs$targ],sep="")
browseURL(directurl)
}
if(key=="x"){
# Print selected genes to terminal and copy systematic gene names to clipboard
printSelected(globs)
if(length(globs$targs)==0){
toClipboard("")
}else{
toClipboard(globs$dat$ORF[globs$targs])
}
}
if(key=="z") {
if(globs$sel==0){
globs$selx=c()
globs$sely=c()
}
globs$sel=(globs$sel+1)%%3
if(globs$sel==2){
# Close polygon
globs$selx=c(globs$selx,globs$selx[1])
globs$sely=c(globs$sely,globs$sely[1])
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}
drawSel(globs$selx,globs$sely)
globs$sel=0
}
}
if(key=="right") {
globs$datno<<-(globs$datno%%length(globs$datlist))+1
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}
globs$orftargs=globs$dat$ORF[globs$targs]
globs$dat=globs$datlist[[globs$datno]]$res
globs$targs=match(globs$orftargs,globs$dat$ORF)
}
if(key=="left") {
globs$datno=((globs$datno-2)%%length(globs$datlist))+1
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}
orftargs=globs$dat$ORF[globs$targs]
globs$dat=globs$datlist[[globs$datno]]$res
globs$targs=match(globs$orftargs,globs$dat$ORF)
}
if(key=="up") {
globs$compno=(globs$compno+1)%%(length(globs$GROUPS$GroupORFs)+1)
#if(globs$compno>length(globs$GROUPS$GroupORFs)) globs$compno=1
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}
}
if(key=="down") {
globs$compno=(globs$compno-1)%%(length(globs$GROUPS$GroupORFs)+1)
#if(globs$compno<=0) globs$compno=length(globs$GROUPS$GroupORFs)
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}
}
return(NULL)
}
visTool<-function(groups,orf2gene,GISfiles,metaRep="MetaReport.txt",fitmax=0,reg="lmreg"){
# Function for generating interactive plot
globs$GROUPS=groups()
globs$ORFGENE=orf2gene
globs$datlist=list()
globs$reg=reg
clients=c()
dates=c()
for (f in 1:length(GISfiles)){
report=getResults(GISfiles[f])
report$res$ratio=pmax(0.005,report$res$QueryFitnessSummary/report$res$ControlFitnessSummary)
report$res$gindex=rank(as.character(report$res$Gene))
report$res$oindex=rank(as.character(report$res$ORF))
report$res$cindex=rank(report$res$ControlFitnessSummary)
report$res$qindex=rank(report$res$QueryFitnessSummary)
report$res$rindex=rank(report$res$QueryFitnessSummary/report$res$ControlFitnessSummary)
#report$datname=paste("Plot",paste(f,":",sep=""),report$summType,"fitness",paste("(",report$testType,")",sep=""))
globs$datlist[[f]]=report
clients=c(clients,report$qCli)
dates=c(dates,report$qDate)
}
# Re-order plots by query client and then by query date
# Takes 22s for 138 datasets...
dlist=unlist(globs$datlist)
dlist=dlist[order(clients,dates)]
dlist=as.list(dlist)
neworder=order(clients,dates)
newDatList=list()
for (i in 1:length(neworder)){
newDatList[[i]]=globs$datlist[[neworder[i]]]
newDatList[[i]]$datname=paste("Plot",paste(i,":",sep=""),newDatList[[i]]$summType,"fitness",paste("(",newDatList[[i]]$testType,")",sep=""))
}
globs$datlist=newDatList
reportExpts(globs,fname=metaRep)
globs$fxmax=c();globs$fymax=c()
globs$fxmin=c();globs$fymin=c()
for(d in globs$datlist){
if(fitmax==0){
globs$fxmax=c(globs$fxmax,d$fMax)
globs$fymax=c(globs$fymax,d$fMax)
}else{
globs$fxmax=c(globs$fxmax,fitmax)
globs$fymax=c(globs$fymax,fitmax)
}
globs$fxmin=c(0,globs$fxmin)
globs$fymin=c(0,globs$fymin)
}
globs$n=0
globs$targs=c()
globs$posits=c()
globs$sel=0
globs$selx=c()
globs$sely=c()
globs$indPoss=c("gindex","oindex","rindex","cindex","qindex")
globs$indNo=0
globs$ind=globs$indPoss[globs$indNo%%length(globs$indPoss)+1]
# Toggling between colour of suppressors and enhancers
globs$ColourScheme=0
globs$Ecol=rgb(0.4,0.4,1)
globs$Scol=rgb(1,0.4,0.4)
globs$ESymbol=25
globs$SSymbol=24
cat("\nControls: Windows mouse\n")
cat("~~~~~~~~~~~~~~~\n")
cat("Left click: Highlight gene/Rotate text position\n")
cat("Right click: Open SGD page for gene (alternatively, press 'w' on keyboard)\n")
cat("Middle click: Remove last gene (alternatively, press 'd' on keyboard)\n\n")
cat("Controls: Mac mouse\n")
cat("~~~~~~~~~~~~~~~\n")
cat("Click: Highlight gene/Rotate text position\n\n")
cat("Controls: Keyboard\n")
cat("~~~~~~~~~~~~~~~\n")
cat("Left/Right arrow: Switch to next/previous fitness plot (comparison between different pair of experiments).\n")
cat("Up/Down arrow: Change group of genes currently highlighted (in purple).\n")
cat("b: Print experimental metadata report to console window\n")
cat("c: Clear highlighting from currently selected genes.\n")
cat("d: Remove highlighting from last gene highlighted.\n")
cat("i: In rank plot mode, toggle between x-axis rank order.\n")
cat("k: In rank plot mode, toggle between fitness ratio, GIS, query fitness and control fitness on y-axis.\n")
cat("l: Toggle plot style between fitness plot (default) and rank plot mode.\n")
cat("p: Save current plot as vector graphic to QFAVisualisation.ps. Other filetypes can also be generated - 'n': .png and 'm': .pdf\n")
cat("q: Quit tool and print gene names currently selected to console window.\n")
cat("r: Enter zoom mode. Click on top left and bottom right of area to inspect (experimental, may have to quit to zoom out...).\n")
cat("s: Highlight genes encircled using select tool ('z').\n")
cat("t: Toggle between colours (blue/red) highlighting positive/negative interactions, and no highlighting.\n")
cat("u: Add new group of genes to list of highlightable groups.\n")
cat("v: Print list of currently selected genes to console and copy standard gene names to clipboard\n")
cat("w: Open SGD web-page for last gene highlighted.\n")
cat("x: Print list of currently selected genes to console and copy systematic gene names to clipboard\n")
cat("z: Toggle select tool on/off. Select genes for highlighting by drawing a polygon on plot. Press 's' to add selection when finished.\n")
globs$datno=1
globs$plotno=1
globs$compno=0
globs$pos=1
globs$zooming=FALSE
globs$zoomTL=c(-99,-99)
globs$zoomBR=c(-99,-99)
globs$rankPlot=FALSE
globs$ratplotyPoss=c("ratio","GIS","QueryFitnessSummary","QueryFitnessSummaryLOG","ControlFitnessSummary","ControlFitnessSummaryLOG")
globs$ratplotIndNo=0
globs$ratploty=globs$ratplotyPoss[globs$ratplotIndNo%%length(globs$ratplotyPoss)+1]
globs$dat=globs$datlist[[globs$datno]]$res
# Check if running under windows, if not, force X11
# Note that event handling doesn't work under Linux :(
sysinf=Sys.info()
#if( sysinf["sysname"]!="Windows") x11()
#if( sysinf["sysname"]=="Linux") Cairo()
x11()
#dev.new()
if(globs$rankPlot){
rnkPlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}else{
makePlot(globs$datno,ecol=globs$Ecol,scol=globs$Scol,esym=globs$ESymbol,ssym=globs$SSymbol)
}
getGraphicsEvent(prompt="Left/Right: Change plot, b: Expt. metadata, L-click: Highlight, M-click: Remove, q: quit", onMouseDown=mouse, onKeybd=keybd)
printSelected(globs)
#if( sysinf["sysname"]!="Windows") dev.off()
dev.off()
}
return(visTool)
}
complexesFromSource<-function(){
# Read in functionally related complexes
# Largely from Benschopp Mol Cell 2010
# Can add some complexes manually
compfile=file.path(system.file(package = "qfa"),"extdata","FunctionalComplexes.txt",sep="")
Complexes=read.delim(compfile,stringsAsFactors=FALSE,sep="\t")
Complexes$CompList=gsub(";"," ",gsub("\\s","",Complexes$Complex.members..systematic.name))
res=data.frame(GroupName=Complexes$X..Complex.name,GroupID="Func.")
res$GroupORFs=Complexes$CompList
return(res)
}
buildComplexes<-function(){
fname=file.path(system.file(package = "qfa"),"extdata","FunctionalComplexes.txt")
cat("\nGroups of functionally related complexes are specified a tab-delimited text file\n which can be found at the path below. This file can be edited with any text editor. Please note that under OSX, this path might be hidden. You can still find and edit the file by copying the path below, opening Finder->Go->Go to File and pasting into the dialogue box.\n")
cat(paste(fname,"\n"))
ComplexesData=read.delim(fname,sep="\t",header=TRUE,stringsAsFactors=FALSE)
return(ComplexesData)
}
buildBenschop<-function() buildComplexes()
iRVisDemo<-function(groupFun=buildComplexes,fitmax=0,reg="lmreg"){
orfile=file.path(file.path(system.file(package = "qfa"),"extdata","ORF2GENE.txt"))
ORFGENE=read.delim(orfile,stringsAsFactors=FALSE,sep="\t",header=FALSE)
colnames(ORFGENE)=c("ORF","Gene")
ORFGENE=ORFGENE[!duplicated(ORFGENE$ORF),]
# Read in GIS files
filenames=list.files(file.path(system.file(package = "qfa"),"extdata"),pattern="\\GIS.txt$",full.names=TRUE)
visTool=makeVisTool()
visTool(groupFun,ORFGENE,filenames,"MetaReport.txt",fitmax=fitmax,reg=reg)
}
NAtoBlank=function(x){
return(ifelse((is.na(x))|(x=="NA"),"",x))
}
getResults<-function(filename){
#print(filename)
# Need to detect at least two different kinds of header now...
fopen=file(filename,"rt")
i=1
while(!grepl("############",readLines(fopen,1))) i=i+1
close(fopen)
cStart=-1 # At what line does control metadata start?
qStart=-1 # At what line does query metadata start?
res=read.delim(filename,skip=i,header=TRUE,stringsAsFactors=FALSE)
hdr=read.delim(filename,nrows=i-1,header=FALSE,stringsAsFactors=FALSE)$V1
for(hdrow in 1:length(hdr)){
if(((grepl("x-axis ",hdr[hdrow]))||(grepl("Control ",hdr[hdrow])))&&(cStart<0)) cStart=hdrow
if(((grepl("y-axis ",hdr[hdrow]))||(grepl("Query ",hdr[hdrow])))&&(qStart<0)) qStart=hdrow
}
qfaVersion=NAtoBlank(strsplit(hdr[1],": ")[[1]][2])
summType=NAtoBlank(strsplit(hdr[2],": ")[[1]][2])
testType=NAtoBlank(strsplit(hdr[3],": ")[[1]][2])
cTreat=NAtoBlank(strsplit(hdr[cStart+0],": ")[[1]][2])
cMed=NAtoBlank(strsplit(hdr[cStart+1],": ")[[1]][2])
cScrID=NAtoBlank(strsplit(hdr[cStart+2],": ")[[1]][2])
cScrNm=NAtoBlank(strsplit(hdr[cStart+3],": ")[[1]][2])
cLibs=NAtoBlank(strsplit(hdr[cStart+4],": ")[[1]][2])
cCli=NAtoBlank(strsplit(hdr[cStart+5],": ")[[1]][2])
cUse=NAtoBlank(strsplit(hdr[cStart+6],": ")[[1]][2])
cDate=NAtoBlank(strsplit(hdr[cStart+7],": ")[[1]][2])
cDate=gsub("'","",cDate)
cDate=gsub('"',"",cDate)
cPI=cCond=cInoc=cFit=""
if(cStart+8<qStart) cPI=NAtoBlank(strsplit(hdr[cStart+8],": ")[[1]][2])
if(cStart+9<qStart) cCond=NAtoBlank(strsplit(hdr[cStart+9],": ")[[1]][2])
if(cStart+10<qStart) cInoc=NAtoBlank(strsplit(hdr[cStart+10],": ")[[1]][2])
if(cStart+11<qStart) cFit=NAtoBlank(strsplit(hdr[cStart+11],": ")[[1]][2])
qTreat=NAtoBlank(strsplit(hdr[qStart+0],": ")[[1]][2])
qMed=NAtoBlank(strsplit(hdr[qStart+1],": ")[[1]][2])
qScrID=NAtoBlank(strsplit(hdr[qStart+2],": ")[[1]][2])
qScrNm=NAtoBlank(strsplit(hdr[qStart+3],": ")[[1]][2])
qLibs=NAtoBlank(strsplit(hdr[qStart+4],": ")[[1]][2])
qCli=NAtoBlank(strsplit(hdr[qStart+5],": ")[[1]][2])
qUse=NAtoBlank(strsplit(hdr[qStart+6],": ")[[1]][2])
qDate=NAtoBlank(strsplit(hdr[qStart+7],": ")[[1]][2])
qDate=gsub("'","",qDate)
qDate=gsub('"',"",qDate)
qPI=qCond=qInoc=qFit=""
if(qStart+8<=length(hdr)) qPI=NAtoBlank(strsplit(hdr[qStart+8],": ")[[1]][2])
if(qStart+9<=length(hdr)) qCond=NAtoBlank(strsplit(hdr[qStart+9],": ")[[1]][2])
if(qStart+10<=length(hdr)) qInoc=NAtoBlank(strsplit(hdr[qStart+10],": ")[[1]][2])
if(qStart+11<=length(hdr)) qFit=NAtoBlank(strsplit(hdr[qStart+11],": ")[[1]][2])
fMax=max(c(res$QueryFitnessSummary,res$ControlFitnessSummary))
qRep=getMode(res$QueryCount)
cRep=getMode(res$ControlCount)
return(
list(res=res,qfaVersion=qfaVersion,summType=summType,testType=testType,
cTreat=cTreat,cMed=cMed,cScrID=cScrID,cScrNm=cScrNm,cLibs=cLibs,cCli=cCli,cUse=cUse,cDate=cDate,cPI=cPI,cCond=cCond,cInoc=cInoc,cFit=cFit,
qTreat=qTreat,qMed=qMed,qScrID=qScrID,qScrNm=qScrNm,qLibs=qLibs,qCli=qCli,qUse=qUse,qDate=qDate,qPI=qPI,qCond=qCond,qInoc=qInoc,qFit=qFit,
fMax=fMax,rept=hdr,qRep=qRep,cRep=cRep)
)
}
toClipboard=function(x,sep="\n"){
# Platform-independent paste-to-clipboard function
x=as.character(x)
if(Sys.info()["sysname"]=="Windows"){
writeClipboard(x)
}else{
osxclipboard <- pipe("pbcopy","w")
write(x,file=osxclipboard,sep=sep)
close(osxclipboard)
}
}
buildGO<-function(){
# Note we do not recommend that users edit this particular set of functionally related genes
fname=file.path(system.file(package = "qfa"),"extdata","GOAnnotation.txt")
cat("\nGrouping of genes by GO terms specified in this text file\n~~~~~~~~~~~~~~~\n")
cat(paste(fname,"\n"))
GO=read.delim(fname,sep="\t",header=TRUE,stringsAsFactors=FALSE)
return(GO)
}
buildPombeGO<-function(){
# Note we do not recommend that users edit this particular set of functionally related genes
fname=file.path(system.file(package = "qfa"),"extdata","pombeGOAnnotation.txt")
cat("\nGrouping of genes by GO terms specified in this text file:\n~~~~~~~~~~~~~~~\n")
cat(paste(fname,"\n"))
GO=read.delim(fname,sep="\t",header=TRUE,stringsAsFactors=FALSE)
return(GO)
}
getText=function(ORFGENE){
x=list()
cat("Input a list of gene names, separated by spaces & press enter:\n")
usergenes=scan(what=character(),nlines=1)
usergenes=toupper(usergenes)
cat("Please input a label for your list of genes (no spaces) & press enter:\n")
lab=scan(what=character(),nlines=1,n=1)
orfs=c()
genes=c()
for(gene in usergenes){
if (gene%in%toupper(ORFGENE$ORF)) {
orfs=c(orfs,gene)
genes=c(genes,ORFGENE$Gene[toupper(ORFGENE$ORF)==gene])
} else {
if(gene%in%toupper(ORFGENE$Gene)){
# Standard gene names are ambiguous
# In this scenario, they do not unambiguously specify species (e.g. RIF1 in cerevisiae and pombe)
orfs=c(orfs,ORFGENE$ORF[toupper(ORFGENE$Gene)==gene])
genes=c(genes,gene)
}
}
}
x[["Genes"]]=genes
x[["ORFs"]]=orfs
x[["Label"]]=lab
print(x)
return(x)
}
drawSel=function(selx,sely){
if(length(selx)==1) {
points(selx,sely,col="black",pch=16,cex=0.4)
}else{
points(selx,sely,col="black",lty=2,type="l")
}
}
printSelected=function(globs){
cat("~~~~~~~~~~~~~~~\n")
cat("\n")
cat("List of genes currently selected:\n")
cat(globs$dat$Gene[globs$targs])
cat("\n")
cat("~~~~~~~~~~~~~~~\n")
cat("\n")
cat("Systematic names for genes currently selected:\n")
cat(globs$dat$ORF[globs$targs])
cat("\n")
cat("\n")
cat("\n")
}
reportExpts=function(globs,fname="MetaReport.txt"){
if(fname!="") {
cat("\nDetailed plot metadata will be written to file:\n")
cat(file.path(getwd(),fname),"\n")
sink(fname)
}
metaSumm=data.frame(PlotNo=numeric(),x.axis=character(),y.axis=character(),stringsAsFactors=FALSE)
for (datno in 1:length(globs$datlist)){
metaSumm[datno,]=c(datno,paste(globs$datlist[[datno]]$cScrNm,globs$datlist[[datno]]$cTreat,globs$datlist[[datno]]$cCond,globs$datlist[[datno]]$cFit),paste(globs$datlist[[datno]]$qScrNm,globs$datlist[[datno]]$qTreat,globs$datlist[[datno]]$qCond,globs$datlist[[datno]]$qFit))
# Print data to console
cat("\nExperimental metadata: plot",datno,"\n")
# Split report string and patch in replicate numbers for Query and Control
rept=globs$datlist[[datno]]$rept
fcont=grep("Control",rept)
if (length(fcont)==0) fcont=grep("x-axis",rept)
findx=tail(fcont,1)
rept2=c(rept[1:findx],paste("x-axis number of replicates:",globs$datlist[[datno]]$cRep),rept[(findx+1):length(rept)],paste("y-axis number of replicates:",globs$datlist[[datno]]$qRep))
strt=4
r2=rept2[strt:length(rept2)]
fin=length(r2)
reptCont=r2[1:(fin/2)]
reptCont=gsub("Control ","",reptCont)
reptQuer=r2[((fin/2)+1):fin]
reptQuer=gsub("Query ","",reptQuer)
df=data.frame(Control=reptCont,Query=reptQuer)
#print(df,row.names=FALSE)
cat(rept2,sep="\n")
}
if(fname!="") sink()
flist=strsplit(fname,"\\.")[[1]]
froot=head(flist,1)
fext=tail(flist,1)
froot2=paste(froot,"Summary",sep="")
fname2=paste(froot2,fext,sep=".")
cat("\nExperimental metadata summary written to file:\n")
cat(file.path(getwd(),fname2),"\n")
cat("\nExperimental metadata summary:\n")
print(metaSumm,row.names=FALSE)
write.table(metaSumm,file=fname2,sep="\t",row.names=FALSE,quote=FALSE)
}
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