Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

annotate phylographics/makeRtrees.pl @ 0:5b9a38ec4a39 draft default tip

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First commit of old repositories
author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
parents:
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1 #!/usr/bin/perl
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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2
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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3 #This script generates an R script to print trees to a pdf file
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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4 #input is a table with treename<tab>newick tree
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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5 use strict;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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6
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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7 my $filename = $ARGV[0];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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8 my $outfile = $ARGV[1];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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9 open FILE, $filename or die $!;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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10 my $treetype = $ARGV[2];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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11 my $extiplabels = $ARGV[3];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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12 my $options;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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13 my $labeltaxfile = $ARGV[4];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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14 my $query = $ARGV[5];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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15 my $midroot = $ARGV[6];
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16 my %labelhash;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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17 my $genecount=0;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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18 my @genes;
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19 my $markquery;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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20 my $midpoint;
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21
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22 if($query eq 'yes'){
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23 $markquery = 1;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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24 }else{
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25 $markquery = 0;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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26 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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27 unless($labeltaxfile eq 'None'){
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28 open LABELFILE, $labeltaxfile or die $!;
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29 while (<LABELFILE>) {
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30 chomp;
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31 #get a line from the data file
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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32 my $currentinput = "$_";
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33 if($currentinput =~ /\t/){
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34 my @splitline = split(/\t/);
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35 my $speciesname= $splitline[0];
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36 $speciesname = "'".$speciesname."'";
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37 my $treename = $splitline[1];
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38 if(exists $labelhash{$treename}){
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39 push @{ $labelhash{$treename} }, $speciesname;
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40 }else{
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41 push @{ $labelhash{$treename} }, $speciesname;
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42 #$labelhash{$treename} = $speciesname;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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43 $genecount ++;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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44 push @genes, $treename;
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45 }
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46 }
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47 }
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48
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49 }#end unless
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50
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51
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52 if($extiplabels eq 'yes'){
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53 $options = ", show.tip.label=FALSE";
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54 }else{
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55 $options = ", show.tip.label=TRUE";
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56 }
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57
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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58 print "require(ape);\n";
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59 print "require(phangorn);\n";
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60 print "pdf(file='$outfile');\n";
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61
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62 while (<FILE>) {
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63 chomp;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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64 #get a line from the data file
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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65 my $currentinput = "$_";
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66 my @splitline = split(/\t/);
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67 my $treename= $splitline[0];
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68 my $tree = $splitline[1];
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69 my $labelsvector;
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70
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71 #print the R commands to make tree graphics
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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72 print "raw_tree <- read.tree(text = '$tree');\n";
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73 print "raw_tree\$edge.length[ is.na(raw_tree\$edge.length) ] <- 0 \n";
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74 if($midroot eq 'yes'){
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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75 print "raw_tree <- midpoint(raw_tree)\n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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76 }
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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77 #Check if large tree, then make text size smaller
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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78 print "thetips <- raw_tree\$tip.label \n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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79 print "numtips <- length(thetips) \n";
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80
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81 #Make text smaller for trees with many tips
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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82 print "if(numtips>250){plot(raw_tree, cex=0.15, edge.width = 0.1, type='$treetype' $options)}else if(numtips>75){plot(raw_tree, cex=0.3, type='$treetype' $options)}else{plot(raw_tree, cex=0.6, type='$treetype' $options)};\n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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83 print "title('Tree File: $treename');\n";
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84
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85 #Add taxon labels, if optional file present and if labels exist for tree
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86 if(exists $labelhash{$treename}){
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87 $labelsvector = join ",", @{ $labelhash{$treename} };
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88 $labelsvector = "tolabel <- c(".$labelsvector.")";
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89 print "thetips <- raw_tree\$tip.label \n";
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90 print $labelsvector."\n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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91 print "labels <- match(tolabel,thetips) \n";
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92 print "tiplabels(tip=labels, pch=21, cex=1) \n";
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93 }
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94
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95
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96 #Add taxon labels if gene name contains QUERY - for readplacement
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97 if($markquery == 1){
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98 print "thetips <- raw_tree\$tip.label \n";
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99 print "qlabels <- grep(\'QUERY\',thetips) \n";
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100 print "tiplabels(tip=qlabels, pch=21, cex=1.1) \n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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101 print "l1labels <- grep(\'LANDMARK1\',thetips) \n";
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102 print "tiplabels(tip=l1labels, pch=15, cex=.8, col='red') \n";
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103 }
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104 }
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105
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106 print "dev.off();\n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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107 close FILE;
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108
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109 #Testing hash arrays
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110 #my %nums;
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111 #my $test='odd';
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112 #for my $n (4,5,6,10) {
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113 # if ($n % 2) {
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114 # push @{ $nums{$test} }, $n;
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115 # } else {
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116 # push @{ $nums{even} }, $n;
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117 # }
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118 #}
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119 #
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120 #print join ', ', @{ $nums{even} };
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121 #print "\n\n";