Mercurial > repos > petr-novak > re_utils

comparison ChipSeqRatioAnalysis.R @ 8:99569eccc583 draft

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author petr-novak
date Mon, 09 Dec 2019 04:14:48 -0500
parents f224513123a1
children
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7:89c5ba120b21 8:99569eccc583
29 29
30 #arguments 30 #arguments
31 args <- commandArgs(trailingOnly = TRUE) 31 args <- commandArgs(trailingOnly = TRUE)
32 input <- args[1] 32 input <- args[1]
33 HTMLfile <- args[2] 33 HTMLfile <- args[2]
34 threshld <- 2/(2+1) 34 thr = 5
35 threshld <- thr/(thr+1)
36
35 inputN=as.numeric(args[3]) 37 inputN=as.numeric(args[3])
36 chipN=as.numeric(args[4]) 38 chipN=as.numeric(args[4])
37 #dataframe preprocessing and table creation 39 #dataframe preprocessing and table creation
38 df <- read.delim(input, comment.char="#") 40 df <- read.delim(input, comment.char="#")
39 41
53 png(pngfile, width = 1000, height = 1200, pointsize=20) 55 png(pngfile, width = 1000, height = 1200, pointsize=20)
54 par(mfrow=c(2,1)) 56 par(mfrow=c(2,1))
55 lims=range(df$"Normalized ratio Chip/Input"[df$"Normalized ratio Chip/Input">0], finite = TRUE) 57 lims=range(df$"Normalized ratio Chip/Input"[df$"Normalized ratio Chip/Input">0], finite = TRUE)
56 suppressWarnings(plot(df$Cluster,df$"Normalized ratio Chip/Input", log="y", xlab="Cluster Nr.", ylab="Normalized ChiP/Input ratio", pch=20, ylim=lims)) 58 suppressWarnings(plot(df$Cluster,df$"Normalized ratio Chip/Input", log="y", xlab="Cluster Nr.", ylab="Normalized ChiP/Input ratio", pch=20, ylim=lims))
57 abline(h=1,col='#00000080', lwd = 2) 59 abline(h=1,col='#00000080', lwd = 2)
58 abline(h=2,col='#FF000080', lwd = 2) 60 abline(h=thr,col='#FF000080', lwd = 2)
59 61
60 62
61 suppressWarnings(plot(df$Cluster,df$"Normalized ratio Chip/(Chip+Input)", xlab="Cluster Nr.", ylab="Normalized Chip/(Chip+Input)", pch=20)) 63 suppressWarnings(plot(df$Cluster,df$"Normalized ratio Chip/(Chip+Input)", xlab="Cluster Nr.", ylab="Normalized Chip/(Chip+Input)", pch=20))
62 abline(h=0.5,col='#00000080', lwd = 2) 64 abline(h=0.5,col='#00000080', lwd = 2)
63 abline(h=threshld,col='#FF000080', lwd = 2) 65 abline(h=threshld,col='#FF000080', lwd = 2)
77 79
78 80
79 HTML(graph, file=filename) 81 HTML(graph, file=filename)
80 if (nrow(outputTable)>0){ 82 if (nrow(outputTable)>0){
81 HTML(outputTable, file=filename, classtable = "dataframe", 83 HTML(outputTable, file=filename, classtable = "dataframe",
82 row.names=FALSE, align='left', caption="Clusters with Normalized ChIP/Input ratio > 2", captionalign="top") 84 row.names=FALSE, align='left', caption=paste("Clusters with Normalized ChIP/Input ratio >", thr), captionalign="top")
83 } 85 }
84 HTMLEndFile(filename) 86 HTMLEndFile(filename)
85 # file.rename(from=filename, to=HTMLfile) 87 # file.rename(from=filename, to=HTMLfile)
86 system(sprintf("cp -r ./%s %s", filename, HTMLfile)) 88 system(sprintf("cp -r ./%s %s", filename, HTMLfile))
87 write.table(df, file=input, sep="\t", row.names = FALSE) 89 write.table(df, file=input, sep="\t", row.names = FALSE)