Mercurial > repos > petr-novak > re_utils
diff ChipSeqRatioAnalysis.R @ 5:378565f5a875 draft
Uploaded
| author | petr-novak |
|---|---|
| date | Fri, 22 Nov 2019 07:56:48 -0500 |
| parents | e320ef2d105a |
| children | f224513123a1 |
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--- a/ChipSeqRatioAnalysis.R Wed Sep 18 06:30:04 2019 -0400 +++ b/ChipSeqRatioAnalysis.R Fri Nov 22 07:56:48 2019 -0500 @@ -3,82 +3,28 @@ library(base64enc, quietly=T) -htmlheader=" - <html xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"> +htmlheader= +" <html xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"> <head> <title> ChIP-Seq Mapper Output </title> - <style> - <!-- - table { background:#FFFFFF; - border:1px solid gray; - border-collapse:collapse; - color:#fff; - font:normal 13px verdana, arial, helvetica, sans-serif; - width: 100%; + <style> +html,body{font-family:Verdana,sans-serif;font-size:15px;line-height:1.5} - } - caption { border:1px solid #5C443A; - color:#5C443A; - font-weight:bold; - font-size:20pt - padding:6px 4px 8px 0px; - text-align:center; - - } - td, th { color:#363636; - padding:.4em; - } - tr { border:1px dotted gray; - } - thead th, tfoot th { background:#5C443A; - color:#FFFFFF; - padding:3px 10px 3px 10px; - text-align:left; - text-transform:uppercase; - } - tbody td a { color:#3636FF; - text-decoration:underline; - } - tbody td a:visited { color:gray; - text-decoration:line-through; - } - tbody td a:hover { text-decoration:underline; - } - tbody th a { color:#3636FF; - font-weight:normal; - text-decoration:none; - } - tbody th a:hover { color:#363636; - } - tbody td+td+td+td a { background-image:url('bullet_blue.png'); - background-position:left center; - background-repeat:no-repeat; - color:#FFFFFF; - padding-left:15px; - } - tbody td+td+td+td a:visited { background-image:url('bullet_white.png'); - background-position:left center; - background-repeat:no-repeat; - } - tbody th, tbody td { text-align:left; - vertical-align:top; - } - tfoot td { background:#5C443A; - color:#FFFFFF; - padding-top:3px; - } - .odd { background:#fff; - } - tbody tr:hover { background:#EEEEEE; - border:1px solid #03476F; - color:#000000; - } - --> - </style> +table { + border-collapse: collapse; + border: 1px solid black; + width: 1000pt +} +table, th, td { + border: 1px solid black; +} +</style> </head> - - " + + + +" #arguments @@ -97,21 +43,20 @@ 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),] +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(3,1)) +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/Seq ratio", pch=20, ylim=lims)) abline(h=1,col='#00000080', lwd = 2) abline(h=2,col='#FF000080', lwd = 2) -lims=range(df$"Normalized ratio Chip/Input", finite = TRUE) -suppressWarnings(plot(df$Cluster,df$"Normalized ratio Chip/Input", xlab="Cluster Nr.", ylab="Normalize ChiP/Seq ratio", pch=20, ylim=lims)) -abline(h=1,col='#00000080', lwd = 2) -abline(h=2,col='#FF000080', lwd = 2) suppressWarnings(plot(df$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) @@ -133,7 +78,8 @@ HTML(graph, file=filename) if (nrow(outputTable)>0){ - HTML(outputTable, file=filename, classtable = "dataframe", row.names=FALSE, Align='left') + HTML(outputTable, file=filename, classtable = "dataframe", + row.names=FALSE, align='left', caption="Clusters with Normalized ChIP/Input ratio > 2", captionalign="top") } HTMLEndFile(filename) file.rename(from=filename, to=HTMLfile)