Mercurial > repos > petr-novak > re_utils
view ChipSeqRatioAnalysis.R @ 25:5dba804e6884 draft
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
author | petr-novak |
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date | Wed, 02 Aug 2023 12:42:08 +0000 |
parents | 99569eccc583 |
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#!/usr/bin/env Rscript library(R2HTML, quietly=T) library(base64enc, quietly=T) htmlheader= " <html xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"> <head> <title> ChIP-Seq Mapper Output </title> <style> html,body{font-family:Verdana,sans-serif;font-size:15px;line-height:1.5} table { border-collapse: collapse; border: 1px solid black; width: 1000pt } table, th, td { border: 1px solid black; } </style> </head> " #arguments args <- commandArgs(trailingOnly = TRUE) input <- args[1] HTMLfile <- args[2] thr = 5 threshld <- thr/(thr+1) inputN=as.numeric(args[3]) chipN=as.numeric(args[4]) #dataframe preprocessing and table creation df <- read.delim(input, comment.char="#") df$"Ratio Chip/Input"=df$Chip_Hits/df$Input_Hits df$"Normalized ratio Chip/Input"=(df$Chip_Hits/chipN)/(df$Input_Hits/inputN) df$"Ratio Chip/(Chip+Input)"=df$Chip_Hits/(df$Chip_Hits + df$Input_Hits) df$"Normalized ratio Chip/(Chip+Input)"=(df$Chip_Hits/chipN)/((df$Input_Hits/inputN)+(df$Chip_Hits/chipN)) outputTable = df[df$"Normalized ratio Chip/(Chip+Input)" > threshld, ] outputTable = outputTable[!is.na(outputTable$Cluster), c('Cluster', 'Chip_Hits', 'Input_Hits', 'Normalized ratio Chip/Input','Normalized ratio Chip/(Chip+Input)')] save.image("tmp.RData") #Plot creation pngfile <- tempfile() png(pngfile, width = 1000, height = 1200, pointsize=20) par(mfrow=c(2,1)) lims=range(df$"Normalized ratio Chip/Input"[df$"Normalized ratio Chip/Input">0], finite = TRUE) suppressWarnings(plot(df$Cluster,df$"Normalized ratio Chip/Input", log="y", xlab="Cluster Nr.", ylab="Normalized ChiP/Input ratio", pch=20, ylim=lims)) abline(h=1,col='#00000080', lwd = 2) abline(h=thr,col='#FF000080', lwd = 2) suppressWarnings(plot(df$Cluster,df$"Normalized ratio Chip/(Chip+Input)", xlab="Cluster Nr.", ylab="Normalized Chip/(Chip+Input)", pch=20)) abline(h=0.5,col='#00000080', lwd = 2) abline(h=threshld,col='#FF000080', lwd = 2) dev.off() graph <- paste('<img src="data:image/png;base64 ,', base64encode(pngfile), '" alt="image" />' ) #HMTL report creation + writing final output directory=dirname(HTMLfile) filename=basename(HTMLfile) ## create HTML header cat(htmlheader, file = filename) HTML(graph, file=filename) if (nrow(outputTable)>0){ HTML(outputTable, file=filename, classtable = "dataframe", row.names=FALSE, align='left', caption=paste("Clusters with Normalized ChIP/Input ratio >", thr), captionalign="top") } HTMLEndFile(filename) # file.rename(from=filename, to=HTMLfile) system(sprintf("cp -r ./%s %s", filename, HTMLfile)) write.table(df, file=input, sep="\t", row.names = FALSE)