Refined support for bubble plots

src/admire

@@ -289,7 +289,7 @@ base = file.path("./")
 results = file.path("results/")
 
 # WORKING ENVIRONMENT BASICS
-sampleInfo = read.450k.sheet(base = base)
+sampleInfo = read.450k.sheet(base = base, pattern="SampleSheet.csv")
 
 # PARAMETERS
 normalization="$N"
@@ -417,7 +417,7 @@ EXCEL=excel
 mkdir -p $EXCEL
 set -- ${groups[@]}
 cat > additional_images.txt << EOL
-file    group   region  chr
+file	group	region	chr
 EOL
 for a; do
         shift

src/renderAdditionalImages.R

@@ -1,7 +1,7 @@
 library("RColorBrewer")
-#source(".Rprofile")
-#source("config.R")
-#source("meth_plot.R")
+source(".Rprofile")
+source("config.R")
+source("meth_plot.R")
 
 driver = read.table("additional_images.txt",header=T,sep="\t", stringsAsFactors = F)
 intervals = data.frame(c(0,.1,.2,.3,.4,.5,.6,.7,.8,.9),c(.1,.2,.3,.4,.5,.6,.7,.8,.9,1))
@@ -21,12 +21,12 @@ for(i in 1:nrow(driver)) {
   betaValues = t(betaValues)
   rownames(betaValues) = sampleInfo[groupSamples,"Sample_Group"]
 
-  png(file=paste(dirname(driver[i,"file"]),"/",driver[i,"chr"],"-",min(probePositions),"-",max(probePositions),".png",sep=""))
+  pdf(file=paste(dirname(driver[i,"file"]),"/",driver[i,"chr"],"-",min(probePositions),"-",max(probePositions),".pdf",sep=""))
   meth_plot(betaValues,intervals,"by-meth","proportional",probePositions,row.names(betaValues),probeNames)
   dev.off()
-  png(file=paste(dirname(driver[i,"file"]),"/hm-",driver[i,"chr"],"-",min(probePositions),"-",max(probePositions),".png",sep=""))
-  meth_plot(betaValues,intervals,"by-meth","grid",probePositions,row.names(betaValues),probeNames)
-  dev.off()
-  #unlink(paste(driver[i,"file"],"txt",sep="."))
+  #pdf(file=paste(dirname(driver[i,"file"]),"/hm-",driver[i,"chr"],"-",min(probePositions),"-",max(probePositions),".pdf",sep=""))
+  #meth_plot(betaValues,intervals,"by-meth","grid",probePositions,row.names(betaValues),probeNames)
+  #dev.off()
+  unlink(paste(driver[i,"file"],"txt",sep="."))
 }