#!/usr/bin/perl
# AmphoraVizu: visualization software for metagenomics analysis tools AMPHORA2 and AmphoraNet
# Copyright (C) 2014 Csaba Kerepesi, Balazs Szalkai, Vince Grolmusz
# AmphoraVizu is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details: .
# For any other inquiries send an Email to Csaba Kerepesi: kerepesics@caesar.elte.hu
# AmphoraVizu webserver: http://pitgroup.org/amphoravizu
# Options:
# -input: input file (AMPHORA2 output file), default: /dev/stdin
# -min_confidence: minimum confidence, default: 0.1
# -lowest_rank: lowest rank (1=Superkingdom, 7=Species), default: 2
# -min_average: minimum average to display, default: 0.02
# -chart_title: chart title (with optional HTML tags), to override default title
# -chart_type: "column": Column Chart output (default), "pie": Pie chart output with averages
# -chart_width: width of chart area, all CSS values are valid (default: 100%)
# -chart_height: height of chart area (default: 100%)
# -chart_compact: if 1, margins are decreased as much as possible (default: 0)
# -html_inline: if 1, tags like , and are omitted (default: 0)
# -miniview: 1: miniview on, 0: miniview off (default: 0)
# -sort: "avg": sorted by averages (default), "abc" sorted by alphabet
# -quantify: "prop": shows the proportions of marker genes (default), "amounts": shows the exact amounts of marker genes
# A typical running command:
# perl AmphoraVizu.pl -input example_output.txt -min_confidence 0.9 -lowest_rank 2 -min_average 0.02 -chart_type column > out.html
my (%avg, %sum, %summarker, %sumphylotype)= ();
my (@phylotypes,@markers);
my $rank="";
my $first=1;
my %args;
my $sum_all_markers=0;
for ($i = 0; $i < @ARGV; $i += 2) {
$args{$ARGV[$i]} = $ARGV[$i+1];
}
my $infile = ((exists $args{"-input"}) ? $args{"-input"} : "/dev/stdin");
my $min_confidence = ((exists $args{"-min_confidence"}) ? $args{"-min_confidence"} : 0.1);
my $lowest_rank = ((exists $args{"-lowest_rank"}) ? $args{"-lowest_rank"} : 2);
my $min_average = ((exists $args{"-min_average"}) ? $args{"-min_average"} : 0.02);
my $chart_title = ((exists $args{"-chart_title"}) ? $args{"-chart_title"} : "Visualization of \$filename (lowest rank: \$lowest_rank, min. confidence: \$min_confidence, min. average: \$min_average)");
my $chart_type = ((exists $args{"-chart_type"}) ? $args{"-chart_type"} : "column");
my $chart_width = ((exists $args{"-chart_width"}) ? $args{"-chart_width"} : "100%");
my $chart_height = ((exists $args{"-chart_height"}) ? $args{"-chart_height"} : "100%");
my $chart_compact = ((exists $args{"-chart_compact"}) ? $args{"-chart_compact"} : 0);
my $html_inline = ((exists $args{"-html_inline"}) ? $args{"-html_inline"} : 0);
my $miniview = ((exists $args{"-miniview"}) ? $args{"-miniview"} : 0);
my $sort = ((exists $args{"-sort"}) ? $args{"-sort"} : "avg");
my $quantify = ((exists $args{"-quantify"}) ? $args{"-quantify"} : "prop");
open (IN, $infile) || die "Can't open $infile";
while () {
if ($first) {
chop;
if (! $_ =~ /^Query\s+Marker\s+Superkingdom\s+Phylum\s+Class\s+Order\s+Family\s+Genus\s+Species$/ ) {
die "Wrong inputfile format. Please use an AMPHORA2 result file as input.\n";
}
$first=0;
} else {
chop;
my @inputline;
my @inputline0 = split /\t/;
my $j=2;
my $i=1;
$inputline[0]=$inputline0[0];
$inputline[1]=$inputline0[1];
while ( (exists $inputline0[$j]) && ($j<=1+$lowest_rank) ) {
if ( $inputline0[$j] =~ /^(.+)\((\d\.\d\d)\)$/ ) {
if ($2 >= $min_confidence){
push @inputline,$1;
push @inputline,$2;
$i=$j;
}
}
$j++;
}
if ($i>1) {
if ($i==2) {
$rank=""
} elsif ($i==3) {
$rank=" Phylum"
} elsif ($i==4) {
$rank= " Class"
} elsif ($i==5) {
$rank=" Order"
} elsif ($i==6) {
$rank=" Family"
} elsif ($i==7) {
$rank=" Genus"
} elsif ($i==8) {
$rank=""
}
my $k=2*$i-2;
$inputline[$k]=$inputline[$k].$rank;
if (!exists $summarker{$inputline[1]}) {
push @markers,$inputline[1];
}
$summarker{$inputline[1]}++;
if (!exists $sumphylotype{$inputline[$k]}) {
push @phylotypes, $inputline[$k];
}
$sumphylotype{$inputline[$k]}++;
$sum{$inputline[1]}{$inputline[$k]}++;
}
}
}
close IN;
foreach my $keym (@markers) {
$sum_all_markers+=$summarker{$keym};
}
$nummarkers = @markers;
$num_disp_phylotypes=0;
foreach my $keyp (@phylotypes) {
foreach my $keym (@markers) {
if (exists $sum{$keym}{$keyp}) {
if ($quantify eq "prop") {
$avg{$keyp}+=$sum{$keym}{$keyp}/$summarker{$keym};
}elsif ($quantify eq "amounts") {
$avg{$keyp}+=$sum{$keym}{$keyp};
}
}
}
if ($quantify eq "prop") {
$avg{$keyp}=$avg{$keyp}/$nummarkers;
}elsif ($quantify eq "amounts") {
$avg{$keyp}=$avg{$keyp}/$sum_all_markers;
}
if ($avg{$keyp} > $min_average) {
$num_disp_phylotypes++;
}
}
my $calc_width=7*$num_disp_phylotypes*$nummarkers;
if (($chart_type eq "column") && ($miniview) && ($calc_width > 1200)) {
printf(qq~Too many columns~);
}else {
if (!$html_inline) {
printf("");
printf("");
printf("AmphoraVizu");
printf("");
}
if($chart_type eq "column") {
&column_chart();
}elsif ($chart_type eq "pie") {
&pie_chart();
}
printf(q||, $chart_type, $chart_width, $chart_height);
if (!$html_inline) {
printf("\n");
printf("\n");
}
}
######################################################################################
sub column_chart {
printf(qq~
~);
}
sub pie_chart {
printf(qq~
~);
}
sub print_chart_options {
if ($lowest_rank==1) {
$lowest_rank="Superkingdom"
} elsif ($lowest_rank==2) {
$lowest_rank="Phylum"
} elsif ($lowest_rank==3) {
$lowest_rank= "Class"
} elsif ($lowest_rank==4) {
$lowest_rank="Order"
} elsif ($lowest_rank==5) {
$lowest_rank="Family"
} elsif ($lowest_rank==6) {
$lowest_rank="Genus"
} elsif ($lowest_rank==7) {
$lowest_rank="Species"
}
my $title=$chart_title;
$title =~ s/\$chart_type/$chart_type/eg;
$title =~ s/\$filename/$infile/eg;
$title =~ s/\$min_average/$min_average/eg;
$title =~ s/\$min_confidence/$min_confidence/eg;
$title =~ s/\$lowest_rank/$lowest_rank/eg;
$title =~ s/\\/\\\\/g;
$title =~ s/"/\\"/g;
printf(q|title:"%s", width:"%s", height:"%s"|, $title, $chart_width, $chart_height);
if ($chart_type eq "column") {
printf(qq~, vAxis: {minValue: 0}~);
}
if ($chart_compact) {
printf(", chartArea: {width:'85%%',height:'80%%'}, legend: {position: 'bottom'}");
}
}