Mercurial > repos > jbrayet > annotatepeaks

changeset 7:f7123cad20d8 draft

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Deleted selected files
author jbrayet
date Thu, 13 Aug 2015 11:17:07 -0400
parents c8a7d0b5bea4
children 375c3d21e8fc
files catDist.R
diffstat 1 files changed, 0 insertions(+), 241 deletions(-) [+]
line wrap: on
line diff
--- a/catDist.R	Thu Aug 13 11:03:14 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,241 +0,0 @@
-#usage $0 STEP RIGHT chipPeaks outputFile.png output.txt [controlPeaks]
-args <- commandArgs(TRUE)
-
-input <- args[2]
-pngFile <- args[3]
-dataTable <-read.table(file=input, header=TRUE);
-chip.data<-data.frame(dataTable)
-ifReg <- 0
-if (length(unique(chip.data$Reg))>1) {
- ifReg <- 1
-}
-
-ifPDF <- 0
-if (length(args)>=5) {
-	ifPDF=args[5]
-}
-if (length(args)==4 & args[4]==1) {
-	ifPDF=1
-}
-
-ifControl <- 0
-if (length(args)>=4 & args[4]!=1 & args[4]!=0) {
-  dataTable <-read.table(file=args[4], header=TRUE);
-  control.data<-data.frame(dataTable)
-  ifControl <- 1
-}
-if (ifReg & ifControl) {
-
-  if (ifPDF==1) {
-	pdf(file = pngFile, width = 14, height = 13, pointsize = 20, bg = "white")
-  } else {
-       png(filename = pngFile, width =  1440, height =  1040, units = "px", pointsize = 20, bg = "white", res = NA)
-	plot(1:10)
-  }
-  op <- par(mfrow = c(3,2))
-} else {
-
-  if (ifPDF==1) {
-	pdf(file = pngFile, width = 22, height = 8, pointsize = 20, bg = "white")
-  } else {
-        png(filename = pngFile, width = 1580, height = 530, units = "px", pointsize = 20, bg = "white", res = NA)
-	plot(1:10)
-  }
-  op <- par(mfrow = c(1,2))
-}
-myColor <- 1
-myColor[1] <- colors()[131]
-myColor[2] <- colors()[59]
-myColor[3] <- colors()[76]
-myColor[4] <- colors()[88]
-myColor[5] <- colors()[17]
-myColor[6] <- colors()[565]
-myColorControl <- 1
-myColorControl[1] <- colors()[24]
-myColorControl[2] <- colors()[278]
-myColorControl[3] <- colors()[305]
-myColorControl[4] <- colors()[219]
-myColorControl[5] <- colors()[343]
-myColorControl[6] <- colors()[245]
-myLevels <- 0
-if (ifReg) {
- 	if (ifControl) {
-	 #control vs real:
-
-		 countTotal <- length(chip.data$Reg)
-		  totalChIP <- summary(chip.data$Type)/countTotal
-		  tt <- which(chip.data$Type=="intragenic")	
-		  subset.chip <- chip.data[tt,]
-		  countIntra <- length(subset.chip$Reg)
-		  intraChip<- summary(subset.chip$TypeIntra)/countTotal
-		  nlev <- length(levels(chip.data$Type))
-		  countTotalCont <- length(control.data$Reg)
-		      totalContr <- summary(control.data$Type)/countTotalCont
-		      tt <- which(control.data$Type=="intragenic")	
-		      subset.control <- control.data[tt,]
-		      countIntraCont <- length(subset.control$Reg)
-		      intraControl<- summary(subset.control$TypeIntra)/countTotalCont
-		      cum = matrix( 0, nrow=2,  ncol=nlev, byrow = TRUE) 
-		      for (i in c(1:nlev)) {	
-			cum[1,i] <- totalChIP[i]
-			cum[2,i] <- totalContr[i]
-		      }
-
-			labels<-c("GeneDown.", "Enh.", "Imm.Down.", "Interg.", "Intrag.", "Prom.")
-			if (length(labels)==length(levels(chip.data$Type))) {
-				barplot(cum,xlab="",beside=TRUE, col=c(myColor[1],colors()[328]), names.arg=labels,ylab="Proportion of peaks")
-			} else {
-		      		barplot(cum,xlab="",beside=TRUE, col=c(myColor[1],colors()[328]), names.arg=c(levels(chip.data$Type)),ylab="Proportion of peaks")
-			}
-
-    			position <- 'topleft'
-     			inset <- c(0.1, 0)
-			legend(position, c("ChIP","Control"), bty="n",fill=c(myColor[1],colors()[328]), inset=inset)
-
-		      nlev <- length(levels(subset.chip$TypeIntra))
-		      cum = matrix( 0, nrow=2,  ncol=nlev, byrow = TRUE) 
-		      for (i in c(1:nlev)) {	
-			cum[1,i] <- intraChip[i]
-			cum[2,i] <- intraControl[i]
-		      }
-		      barplot(cum,xlab="",beside=TRUE, col=c(myColor[1],colors()[328]), names.arg=c(levels(subset.chip$TypeIntra)),ylab="Proportion of peaks")
-
-			position <- 'topleft'
-     			inset <- c(0.1, 0)
-			legend(position, c("ChIP","Control"), bty="n",fill=c(myColor[1],colors()[328]), inset=inset)
-	}
-	 n.types <- length(levels(chip.data$Reg))
-	 myLevels <- levels(chip.data$Reg)
-	 nlev <- length(levels(chip.data$Type))
-         cum = matrix( 0, nrow=length(myLevels),  ncol=nlev, byrow = TRUE) 
-         countTotal <- length(chip.data$Reg)
-	 colReg <-NULL
-         for (r in c(1:length(myLevels))) {
-	      tt <- which(chip.data$Reg==myLevels[r])
-              totalChIP <- summary(chip.data$Type[tt])/countTotal
-	      for (i in c(1:nlev)) {	
-		cum[r,i] <- totalChIP[i]                
-	      }
-	      colReg[r]<-myColor[r+3]
-         }
-
-	labels<-c("GeneDown.", "Enh.", "Imm.Down.", "Interg.", "Intrag.", "Prom.")
-	if (length(labels)==length(levels(chip.data$Type))) {
-		#barplot(cum,xlab="",beside=TRUE, col=c(myColor[1],myColor[5]), names.arg=labels,ylab="Proportion of peaks")
-		barplot(cum,xlab="",beside=TRUE, col=c(colReg), names.arg=labels,ylab="Proportion of peaks")
-	} else {
-		barplot(cum,xlab="",beside=TRUE, col=c(colReg), names.arg=c(levels(chip.data$Type)),ylab="Proportion of peaks")
-	}
-
-    	position <- 'topleft'
-     	inset <- c(0.1, 0)
-	legend(position, c(myLevels), bty="n",fill=c(colReg), inset=inset)
-
-
-	 nlev <- length(levels(chip.data$TypeIntra))
-         cum = matrix( 0, nrow=length(myLevels),  ncol=nlev, byrow = TRUE) 	 
-         for (r in c(1:length(myLevels))) {
-	      tt <- which(chip.data$Reg==myLevels[r]&chip.data$Type=="intragenic")
-              totalChIP <- summary(chip.data$TypeIntra[tt])/countTotal
-	      for (i in c(1:nlev)) {	
-		cum[r,i] <- totalChIP[i]                
-	      }	      
-         }
-         barplot(cum,xlab="",beside=TRUE, col=c(colReg), names.arg=c(levels(chip.data$TypeIntra)),ylab="Proportion of peaks")
-	position <- 'topleft'
-     	inset <- c(0.1, 0)
-	legend(position, c(myLevels), bty="n",fill=c(colReg), inset=inset)
-
-	 
-	 if (ifControl) {
-		nlev <- length(levels(control.data$Type))
-		cum = matrix( 0, nrow=length(myLevels),  ncol=nlev, byrow = TRUE) 
-		 countTotal <- length(control.data$Reg)
-		 colReg <-NULL
-		 for (r in c(1:length(myLevels))) {
-		      tt <- which(control.data$Reg==myLevels[r])
-		      totalcontrol <- summary(control.data$Type[tt])/countTotal
-		      for (i in c(1:nlev)) {	
-			cum[r,i] <- totalcontrol[i]                
-		      }
-		      colReg[r]<-myColorControl[r+3]
-		 }
-		labels<-c("GeneDown.", "Enh.", "Imm.Down.", "Interg.", "Intrag.", "Prom.")
-		if (length(labels)==length(levels(chip.data$Type))) {
-			barplot(cum,xlab="",beside=TRUE, col=c(colReg), names.arg=labels,ylab="Proportion of peaks")
-		} else {
-		 	barplot(cum,xlab="",beside=TRUE, col=c(colReg), names.arg=c(levels(control.data$Type)),ylab="Proportion of peaks")
-		}
-		position <- 'topleft'
-	     	inset <- c(0.1, 0)
-		legend(position, c(myLevels), bty="n",fill=c(colReg), inset=inset)
-
-		 nlev <- length(levels(control.data$TypeIntra))
-		 cum = matrix( 0, nrow=length(myLevels),  ncol=nlev, byrow = TRUE) 	 
-		 for (r in c(1:length(myLevels))) {
-		      tt <- which(control.data$Reg==myLevels[r]&control.data$Type=="intragenic")
-		      totalcontrol <- summary(control.data$TypeIntra[tt])/countTotal
-		      for (i in c(1:nlev)) {	
-			cum[r,i] <- totalcontrol[i]                
-		      }		      
-		 }
-		 barplot(cum,xlab="",beside=TRUE, col=c(colReg),  names.arg=c(levels(control.data$TypeIntra)),ylab="Proportion of peaks")	   
-		position <- 'topleft'
-	     	inset <- c(0.1, 0)
-		legend(position, c(myLevels), bty="n",fill=c(colReg), inset=inset)
-	 }
-} else {
-  countTotal <- length(chip.data$Reg)
-  totalChIP <- summary(chip.data$Type)/countTotal
-  tt <- which(chip.data$Type=="intragenic")	
-  subset.chip <- chip.data[tt,]
-  countIntra <- length(subset.chip$Reg)
-  intraChip<- summary(subset.chip$TypeIntra)/countTotal
-  nlev <- length(levels(chip.data$Type))
- if (ifControl) {
-      countTotalCont <- length(control.data$Reg)
-      totalContr <- summary(control.data$Type)/countTotalCont
-      tt <- which(control.data$Type=="intragenic")	
-      subset.control <- control.data[tt,]
-      countIntraCont <- length(subset.control$Reg)
-      intraControl<- summary(subset.control$TypeIntra)/countTotalCont
-      cum = matrix( 0, nrow=2,  ncol=nlev, byrow = TRUE) 
-      for (i in c(1:nlev)) {	
-	cum[1,i] <- totalChIP[i]
-	cum[2,i] <- totalContr[i]
-      }
-
-      labels<-c("GeneDown.", "Enh.", "Imm.Down.", "Interg.", "Intrag.", "Prom.")
-      if (length(labels)==length(levels(chip.data$Type))) {
-		#barplot(cum,xlab="",beside=TRUE, col=c(myColor[1],myColor[5]), names.arg=labels,ylab="Proportion of peaks")
-	 barplot(cum,xlab="",beside=TRUE, col=c(myColor[1],colors()[328]), names.arg=labels,ylab="Proportion of peaks")
-       } else {
-     	 barplot(cum,xlab="",beside=TRUE, col=c(myColor[1],colors()[328]), names.arg=c(levels(chip.data$Type)),ylab="Proportion of peaks")
-       }
-
-    	position <- 'topleft'
-     	inset <- c(0.1, 0)
-	legend(position,c("ChIP","Control"), bty="n",fill=c(myColor[1],colors()[328]), inset=inset)
-
-      nlev <- length(levels(subset.chip$TypeIntra))
-      cum = matrix( 0, nrow=2,  ncol=nlev, byrow = TRUE) 
-      for (i in c(1:nlev)) {	
-	cum[1,i] <- intraChip[i]
-	cum[2,i] <- intraControl[i]
-      }
-      barplot(cum,xlab="",beside=TRUE, col=c(myColor[1],colors()[328]), names.arg=c(levels(subset.chip$TypeIntra)),ylab="Proportion of peaks")	
-	position <- 'topleft'
-     	inset <- c(0.1, 0)
-	legend(position,c("ChIP","Control"), bty="n",fill=c(myColor[1],colors()[328]), inset=inset)
-
-   } else {
-	labels<-c("GeneDown.", "Enh.", "Imm.Down.", "Interg.", "Intrag.", "Prom.")
-	if (length(labels)==length(levels(chip.data$Type))) {
-		barplot(totalChIP,xlab="", col=myColor, names.arg=labels,ylab="Proportion of peaks")
-	} else {
-      		barplot(totalChIP,xlab="", col=myColor,ylab="Proportion of peaks")
-	}
-        barplot(intraChip,xlab="", col=myColor,ylab="Proportion of peaks")
-   }
-}
-dev.off()