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list2venn.pl
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list2venn.pl
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#!/usr/bin/env perl
=encoding utf8
=head2 Description
list2venn.pl - Convert list of genelist to venn diagrams
=head2 Usage
perl list2venn.pl list_file.txt
R --no-save < list_file.R
=head2 list file format (tsv)
list | genelist file
------------|------------------------------------------------
up_E2 | geneset.DUTERTRE_ESTRADIOL_RESPONSE_24HR_UP.txt
down_E2 | geneset.DUTERTRE_ESTRADIOL_RESPONSE_24HR_DN.txt
E2F_targets | geneset.HALLMARK_E2F_TARGETS.txt
=head3 Output
R script that generate venn diagrams
=head2 Notes
Require gplots, Vennerable and UpSetR packages:
* https://cran.r-project.org/web/packages/gplots
* https://github.com/js229/Vennerable
* https://cran.r-project.org/web/packages/UpSetR/index.html
=cut
use strict;
use warnings;
use Pod::Usage;
## check parameters
my($file) = @ARGV;
die "must provide a list of list as 1st parameter...\n" unless $file;
my $cmd_line = join(" ","list2venn.pl", @ARGV);
## gene names to skip
my %na = ( "na" => 1, "NA" => 1, "#N/A" => 1, "---" => 1, "--" => 1, "-" => 1, " " => 1);
## read lists of genes
my %list_data;
open(F,"<",$file) or die "could not read list of list $file: $!\n";
while(my $line = <F>){
chomp($line);
my ($name,$list) = split(/\t/,$line);
if(not(defined($name))){ next;}
if(not(defined($list))){ next;}
$name =~ s/ /_/g;
print STDERR "reading $name --> $list \n";
open(L,"<",$list) or die "could not read list $list: $!\n";
my @clist ;
while (my $line= <L>){
chomp($line);
# skipp na genes
if(not(defined($line))) {next;}
if($line eq "") {next;}
if($na{$line}) {next;}
push(@clist,$line);
}
# rm duplicates
my %seen = ();
my @unique = grep { ! $seen{ $_ }++ } @clist;
$list_data{$name} = join("::",@unique);
close(L);
}
close(F);
## format lists for Vennerable
# R list
my $gene_lists = "";
foreach my $name (sort keys %list_data){
$gene_lists .= $name."=c(\"".join("\",\"",split(/::/,$list_data{$name}))."\")\n";
}
## format list for gplots
# list1 list2
# gene1 0 1
# gene2 1 1
my %list_item; # eg. genes in all list
my %list_has_item; # eg. name::gene
foreach my $name (sort keys %list_data){
foreach my $item ( split(/::/,$list_data{$name}) ){
$list_has_item{$name."::".$item} = 1;
$list_item{$item} = 1;
}
}
my $gplot_file = $file;
$gplot_file =~ s/.txt//g;
$gplot_file .= ".gplot";
open(VG,">",$gplot_file) or die "could not create gplot data file... \n";
print VG join("\t","gene",sort keys(%list_data)),"\n";
foreach my $item (keys %list_item ){
my @line;
push(@line,$item);
foreach my $name (sort keys %list_data){
if(defined($list_has_item{$name."::".$item})){ push(@line,"1"); }
else{push(@line,"0"); }
}
print VG join("\t",@line)."\n";
}
close(VG);
## name to use for the lists in R
my $names = join(",",sort keys(%list_data) );
my $catnames = "\"".join("\",\"",sort keys(%list_data) )."\"";
my $list_count = keys %list_data;
die "can only generate venn diagrams for 2 or more lists (# list : $list_count) ... \n" unless $list_count >= 2;
## generate R script
my $R_script = $file;
$R_script =~ s/.txt//g;
$R_script .= ".R";
open(R,">",$R_script) or die "could NOT create R script \"$R_script\": $! \n";
print R <<END_R;
# $cmd_line
require("gplots")
require("Vennerable")
require("UpSetR")
par(ps=10)
## lists
$gene_lists
x = list(
$names
)
category = c($catnames)
if(length(category) < 2){
stop( "need at least 2 lists...")
}
##########################################
# gplots : max 5
# https://cran.r-project.org/web/packages/gplots
d = read.table(file="$gplot_file",row.names=1,sep="\t",header=TRUE)
if(length(category) <= 5){
try({
venn(d)
},silent=TRUE)
}else{ print("skipping gplots (> 5 lists) ...")}
###########################################
# Vennerable : max 9
# https://github.com/js229/Vennerable
if(length(category) <= 9){
w <- Venn(Sets=x,SetNames=c($catnames) )
# param: type = "circles" , "squares", "ellipses", "triangles" , "AWFE" or "ChowRuskey"
try({ plot(w, doWeights = FALSE) },silent=TRUE)
try({ plot(w, doWeights = TRUE,type = "circles") },silent=TRUE)
try({ plot(w, doWeights = FALSE,type = "circles") },silent=TRUE)
try({ plot(w, doWeights = TRUE,type = "squares") },silent=TRUE)
try({ plot(w, doWeights = TRUE,type = "ellipses")},silent=TRUE)
try({ plot(w, doWeights = TRUE,type = "triangles") },silent=TRUE)
try({ plot(w, doWeights = TRUE,type = "AWFE") },silent=TRUE)
try({ plot(w, doWeights = TRUE,type = "ChowRuskey") },silent=TRUE)
}else{ print("skipping Vennerable (> 9 lists) ...")}
##########################################
# UpSetR : A More Scalable Alternative to Venn and Euler Diagrams for Visualizing Intersecting Sets
# https://cran.r-project.org/web/packages/UpSetR/index.html
upset(d, sets.bar.color = "#56B4E9", nsets = length(category), nintersects = 60, order.by = "freq", empty.intersections = "off", show.numbers = T )
##########################################
# heatmap
# par(ps=13)
# corgene = cor(x=d,y=NULL, use = "complete.obs",method = c("pearson"))
# nrcol <- 24
# heatmap.2(corgene,revC=TRUE, margins =c(12,9),cellnote = format(round(corgene, digits=2), nsmall = 2),notecol="darkgray", col = rev(colorRampPalette(brewer.pal(10, "RdBu"))(nrcol)), scale="none", key=TRUE, symkey=FALSE, density.info="none", trace="none", cexRow=0.70,cexCol=0.70, tracecol = "black", dendrogram=c("row"), main="heatmap pearson correlation" )
# heatmap.2(corgene,revC=TRUE, margins =c(12,9),cellnote = format(round(corgene, digits=2), nsmall = 2),notecol="black", col=topo.colors(nrcol), scale="none", key=TRUE, symkey=FALSE, density.info="none",trace="none", tracecol="black", dendrogram=c("row"),cexRow=0.70,cexCol=0.70, main="heatmap pearson correlation")
# q(status = 1)
END_R
close(R);
print STDOUT "\n#Run:\nR --no-save < $R_script \n";
exit(0);
=head2 Authors
David Laperriere [email protected]
=cut