R_saving_multiple_plots

R_saving_multiple_plots

# USING "ggplot2" and "for loop"

types <- data.frame(c(rep("breast.C",793),rep("breast.N",97),
                   rep("colon.C",313),rep("colon.N",38),
                   rep("kidney.C",324),rep("kidney.N",160),
                   rep("liver.C",377),rep("liver.N",50),
                   rep("lung.C",473),rep("lung.N",32),
                   rep("prostate.C",502),rep("prostate.N",50)))
colnames(types) <- "types"

tissues <- data.frame(c(rep("breast",890),rep("colon",351),
                      rep("kidney",484),rep("liver",427),
                      rep("lung",505), rep("prostate.C",552)))
colnames(tissues) <- "tissues"

hm <- read.csv("file:///E:/LAB_DATA/00-LabData/Lab/00--Archive/TCGA_DNA_met/423CpGs_set12357/423CpGs.heatmap.with.normal.csv",
               header=F, row.names=1)

dta_hm <- cbind(tissues,types,t(hm))
dim(dta_hm)

library(ggplot2)
setwd("E:/LAB_DATA/00-LabData/Lab/00--Archive/TCGA_DNA_met/423CpGs_set12357/boxplot_with_normal")

colNames <- names(dta_hm)[3:425]
for(i in colNames){
  print(i)
  p <- ggplot(dta_hm, aes_string(x=dta_hm[,2], y=i))
  p + theme_bw() + geom_violin(aes(fill=types), alpha=0.4, scale="width") + geom_boxplot(width=0.4, alpha=0.9,outlier.shape = NA) + theme(axis.text.x=element_text(angle=90,hjust=1,vjust=0.5)) + guides(fill=FALSE) + xlab("") + ylim(0,1)
  ggsave(filename=paste(i,".png",sep=""), width = 5.5, height = 4, dpi = 600)
  graphics.off()
}

+ geom_jitter(width=0.2,alpha=0.3) 

######################
# USING generic R plot functions
setwd("E:/LAB_DATA/00-LabData/Lab/00--Archive/TCGA_DNA_met/423CpGs_set12357/")

dta <- read.csv("file:///E:/LAB_DATA/00-LabData/Lab/00--Archive/TCGA_DNA_met/423CpGs_set12357/423CpGs.boxplot.2.csv", header = T)
file <- "cpg.list.csv"

close(con)
dev.off()
close(con)
dev.off()

con <- file(description=file, open="r")
while (length(line <- readLines(con, n = 1, warn = FALSE)) > 0) {
  print(line)
  dta1 <- dta[,grep(line,colnames(dta))]
  tiff(paste(line,'.tif',sep = ""),units = "px",width = 500, height = 400)
  par(mar=c(3,3,3,3))
  stripchart(dta1, method='jitter', vertical=T, pch=20,cex=.9,
             col=(c(rgb(.8,.8,.3,.7),rgb(.3,.8,.8,.7))),axes = F,
             jitter=.2, ylim=c(-0.1, 1.1))
  b<-boxplot(dta1, las=2, col=(c(rgb(.8,.3,.3,.5),rgb(.3,.3,.8,.5))), add = T,
             main=paste(line), outline=F, xaxt="n")
  lines(b$stats[3,], lwd = 2, lty = 5, type = "o")
  dev.off()
}
close(con)
dev.off()