Mercurial > repos > petr-novak > re_utils

comparison ChipSeqRatioAnalysis.R @ 6:f224513123a1 draft

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author petr-novak
date Mon, 02 Dec 2019 03:45:28 -0500
parents 378565f5a875
children 99569eccc583
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5:378565f5a875 6:f224513123a1
51 save.image("tmp.RData") #Plot creation 51 save.image("tmp.RData") #Plot creation
52 pngfile <- tempfile() 52 pngfile <- tempfile()
53 png(pngfile, width = 1000, height = 1200, pointsize=20) 53 png(pngfile, width = 1000, height = 1200, pointsize=20)
54 par(mfrow=c(2,1)) 54 par(mfrow=c(2,1))
55 lims=range(df$"Normalized ratio Chip/Input"[df$"Normalized ratio Chip/Input">0], finite = TRUE) 55 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/Seq ratio", pch=20, ylim=lims)) 56 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) 57 abline(h=1,col='#00000080', lwd = 2)
58 abline(h=2,col='#FF000080', lwd = 2) 58 abline(h=2,col='#FF000080', lwd = 2)
59 59
60 60
61 suppressWarnings(plot(df$Cluster,df$"Normalized ratio Chip/(Chip+Input)", xlab="Cluster Nr.", ylab="Normalized Chip/(Chip+Input)", pch=20)) 61 suppressWarnings(plot(df$Cluster,df$"Normalized ratio Chip/(Chip+Input)", xlab="Cluster Nr.", ylab="Normalized Chip/(Chip+Input)", pch=20))
80 if (nrow(outputTable)>0){ 80 if (nrow(outputTable)>0){
81 HTML(outputTable, file=filename, classtable = "dataframe", 81 HTML(outputTable, file=filename, classtable = "dataframe",
82 row.names=FALSE, align='left', caption="Clusters with Normalized ChIP/Input ratio > 2", captionalign="top") 82 row.names=FALSE, align='left', caption="Clusters with Normalized ChIP/Input ratio > 2", captionalign="top")
83 } 83 }
84 HTMLEndFile(filename) 84 HTMLEndFile(filename)
85 file.rename(from=filename, to=HTMLfile) 85 # file.rename(from=filename, to=HTMLfile)
86 system(sprintf("cp -r ./%s %s", filename, HTMLfile))
86 write.table(df, file=input, sep="\t", row.names = FALSE) 87 write.table(df, file=input, sep="\t", row.names = FALSE)