Mercurial > repos > petr-novak > re_utils
diff RM_html_report.R @ 0:a4cd8608ef6b draft
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| author | petr-novak |
|---|---|
| date | Mon, 01 Apr 2019 07:56:36 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/RM_html_report.R Mon Apr 01 07:56:36 2019 -0400 @@ -0,0 +1,169 @@ +#!/usr/bin/env Rscript +### this script is expected to run from clustering directory! ###### + +## assume RM-custom_output_tablesummary.csv file in active directory + +suppressPackageStartupMessages(library(R2HTML)) +###################################################################################### +htmlheader=" + <html xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"> + <head> + <title> Clustering summary </title> + <style> + <!-- + table { background:#FFFFFF; + border:1px solid gray; + border-collapse:collapse; + color:#fff; + font:normal 10px verdana, arial, helvetica, sans-serif; + } + 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> + + </head> + + " +###################################################################################### +###################################################################################### + + + +#basic statistics: +# Number of reads used for clustering + +RM=read.table("RM-custom_output_tablesummary.csv",sep="\t",header=TRUE,as.is=TRUE,check.names=FALSE) + +#Any hits to RM database? +N=NA + +# convert to legible format: +RM2=data.frame( + 'total length [bp]'=RM$All_Reads_Length[c(T,F,F)], + 'number of reads'=RM$All_Reads_Number[c(T,F,F)], + check.names=FALSE,stringsAsFactors=FALSE +) + +RMpart1=RM[c(T,F,F),-c(1:3),drop=FALSE] #counts +RMpart2=RM[c(F,T,F),-c(1:3),drop=FALSE] #percent + +RMjoined=list() + +for (i in colnames(RMpart1)){ + RMjoined[[i]]=paste(RMpart1[,i],"hits, ",signif(RMpart2[,i],3),"%",sep='') +} + + + +if (ncol(RM)>3){ # not emppty + RM2=cbind(cluster=paste("CL",1:nrow(RM2),sep=''), + RM2, + "Genome proportion[%]"=signif(RM2$'number of reads'/N*100,3), + "cumulative GP [%]"=signif(cumsum(RM2$'number of reads'/N*100),3), + as.data.frame(RMjoined,stringsAsFactors=FALSE)) + + ##### RM2 formating for html output: ##### + ########################################## + bold=RMpart2>3 + for (i in 6:ncol(RM2)){ + rmcol=RM2[,i] + RM2[,i]=ifelse(bold[,i-5],paste("<b>",rmcol,"</b>",sep=''),rmcol) + } + + # join hits to one column + RMstring=character(nrow(RM2)) + for (i in 1:nrow(RM2)){ + x=ifelse(RMpart2[i,]>0,paste(colnames(RM2[,-(1:5),drop=FALSE])," (",RM2[i,-(1:5),drop=FALSE],")",sep=''),"") + # reorder based on GR + x=x[order(RMpart2[i,],decreasing=TRUE)] + + RMstring[i]=paste(x[x!=''],collapse="<br />") + if (nchar(RMstring[i])>240){ + RMstring[i]=paste(substring(RMstring[i],1,220),"......",sep='') + } + + } +}else{ # no RM hits + RM2=cbind(cluster=paste("CL",1:nrow(RM2),sep=''), + RM2, + "Genome proportion[%]"=signif(RM2$'number of reads'/N*100,3), + "cumulative GP [%]"=signif(cumsum(RM2$'number of reads'/N*100),3)) + RMstring=rep("",nrow(RM)/3) +} + + +# RM2 add link to subpage + + +RM2=data.frame(RM2[,1:3],'Repeat Masker'=RMstring,check.names=FALSE) + + +################################################################################################## +#################### HTML output ##### +################################################################################################## + + +htmlout=commandArgs(T)[1] # full absolute path + +cat(htmlheader,file=htmlout) + +HTML.title("RepeatMasker search against custom database",file=htmlout,HR=1) + +HTML(RM2,file=htmlout,align='left',caption="",captionalign='') +HTMLEndFile(htmlout) +