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comparison GALAXY_FILES/tools/EMBER/Make_Logo_Galaxy.pl @ 3:037c3edda16e

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author mmaiensc
date Thu, 22 Mar 2012 13:49:52 -0400
parents 003f802d4c7d
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2:1a84b8178b45 3:037c3edda16e
1 #!/usr/bin/perl
2 # make a logo-ish gnu-plottable representation of a score matrix
3
4 use Getopt::Long;
5
6 #
7 # command line arguments
8 #
9 $options = "Usage: ./Make_Logo.pl <OPTIONS>
10 -m .model file from EMBER (required)
11 -c comparison list (used to make labels for the x-axis)
12 -o output (required)
13 -a include comparisons not used by EMBER (preceded by # in the .model file: y or n, default n)
14 -f image file format (default 1)
15 1 - eps
16 2 - cgm
17 -k key on/off (y or n, default y)
18 -lx x labels on/off (y or n, default y)
19 -ly y labels on/off (y or n, default y)
20 -yr set yrange manually (enter <min>,<max>, e.g. -1.5,3.5; default chosen automatically)
21 \n";
22
23 $m = "";
24 $c = "";
25 $o = "";
26 $a = "n";
27 $f = 1;
28 $k = "y";
29 $lx= "y";
30 $ly= "y";
31 $yr= "zzzzzzzzzzz";
32
33 GetOptions('m=s' => \$m,
34 'c=s' => \$c,
35 'o=s' => \$o,
36 'a=s' => \$a,
37 'f=i' => \$f,
38 'k=s' => \$k,
39 'lx=s'=> \$lx,
40 'ly=s'=> \$ly,
41 'yr=s'=> \$yr
42 ) || die "\n$options";
43
44 if( $m eq "" ){
45 print "Error: set a value for -m\n\n$options";
46 exit;
47 }
48 if( $o eq "" ){
49 print "Error: set a value for -o\n\n$options";
50 exit;
51 }
52 if( $f != 1 && $f != 2 ){
53 print "Error: set -f to be 1 or 2\n\n$options";
54 exit;
55 }
56 if( $a ne "y" && $a ne "n" ){
57 print "Error: set -a to be y or n\n\n$options";
58 exit;
59 }
60 if( $k ne "y" && $k ne "n" ){
61 print "Error: set -k to be y or n\n\n$options";
62 exit;
63 }
64 if( $lx ne "y" && $lx ne "n" ){
65 print "Error: set -lx to be y or n\n\n$options";
66 exit;
67 }
68 if( $ly ne "y" && $ly ne "n" ){
69 print "Error: set -ly to be y or n\n\n$options";
70 exit;
71 }
72 if( $yr ne "zzzzzzzzzzz" && $yr !~ /,/ ){
73 print "Error: if setting -yr, choose a range delimited by a comma\n\n$options";
74 exit;
75 }
76
77 @parts = split('\.',$m);
78 $name = $o;
79 #for($i=1; $i< $#parts; $i++){
80 # $name = sprintf("%s.%s", $name, $parts[$i]);
81 #}
82
83 #
84 # read in matrix
85 #
86 open(IN,"$m") || die "Error: can't open file $m\n";
87 @re = ();
88 @mat = ();
89
90 # burn 2 lines
91 $line = <IN>;
92 $line = <IN>;
93
94 @coloffs = ();
95 while($line = <IN>){
96 chomp($line);
97 @parts = split(' ',$line);
98 if( ($a eq "n" && $parts[0] !~ /#/) || $a eq "y" ){
99 push(@coloffs, 1 );
100 ($ind, $reval) = split(',', $parts[0]);
101 if( $reval eq "nan" ){$reval = 0.0;}
102 push(@re, $reval);
103 @tmp = ();
104 for($i=1; $i<= $#parts; $i++){
105 if( $parts[$i] eq "NA" ){
106 $parts[$i] = 0.0;
107 }
108 push(@tmp, $parts[$i]);
109 }
110 push(@mat, [@tmp] );
111 }
112 else{
113 push(@coloffs, 0);
114 }
115 }
116 close(IN);
117
118 #
119 # rescale matrix so it's between 0 and 1, then multiply by re
120 #
121 for($i=0; $i<= $#mat; $i++){
122 $min = $mat[$i][0];
123 $max = $mat[$i][0];
124 for($j=1; $j< 5; $j++){
125 if( $min > $mat[$i][$j] ){ $min = $mat[$i][$j]; }
126 if( $max < $mat[$i][$j] ){ $max = $mat[$i][$j]; }
127 }
128 for($j=0; $j< 5; $j++){
129 if( $max != $min ){
130 $mat[$i][$j] = $re[$i]*(($mat[$i][$j]-$min)/($max-$min));
131 }
132 else{
133 $mat[$i][$j] = 0;
134 }
135 }
136 }
137
138
139 #
140 # print out in stacked format
141 #
142 open(OUT,">$name.logo");
143 for($i=0; $i<= $#mat; $i++){
144 $posn = ($mat[$i][0] + $mat[$i][1] + 0.5*$mat[$i][2]);
145 printf OUT ("%f ", -0.5*$mat[$i][2]);
146 printf OUT ("%f ", -$mat[$i][3]);
147 printf OUT ("%f ", -$mat[$i][4]);
148 printf OUT ("%f ", 0.5*$mat[$i][2]);
149 printf OUT ("%f ", $mat[$i][1]);
150 printf OUT ("%f ", $mat[$i][0]);
151 printf OUT ("0 0 0 0 0\n");
152 }
153 close(OUT);
154
155 #
156 # make gnu-plotable file
157 #
158
159 # possibly read in conditions to define xtics
160 $tics = "";
161 if( $c ne "" ){
162 open(IN,"$c") || die "Error: can't open file $c\n";
163 @comps = ();
164 $i = 0;
165 while($line = <IN>){
166 chomp($line);
167 @parts = split(' ',$line);
168 if( $#parts != 1 ){
169 print "Error: comparisons list does not have 2 columns\n";
170 exit;
171 }
172 if( $coloffs[$i] == 1 ){
173 $val = sprintf("%s vs %s", $parts[0], $parts[1]);
174 push(@comps, $val);
175 }
176 $i++;
177 }
178 $tics = "set xtics(\"$comps[0]\" 0";
179 for($i=1; $i<= $#comps; $i++){
180 $tics = sprintf("%s, \"%s\" %i", $tics, $comps[$i], $i);
181 }
182 $tics = sprintf("%s)\nset xtics rotate by -45", $tics);
183 }
184
185 # choose format
186 if( $f == 1 ){
187 $format = "postscript eps color 24";
188 $suff = "eps";
189 }
190 if( $f == 2 ){
191 $format = "cgm \"Helvetica\" 14";
192 $suff = "cgm";
193 }
194
195 # set xrange min and max
196 $min = -0.5;
197 $max = $#mat+0.5;
198
199 # possibly turn off key, xlabel, ylabel
200 $keytoggle = "";
201 $xtoggle = "";
202 $ytoggle = "";
203 if( $k eq "n" ){
204 $keytoggle = "unset key";
205 }
206 if( $lx eq "n" ){
207 $xtoggle = "unset xtics";
208 }
209 if( $ly eq "n" ){
210 $ytoggle = "unset ylabel";
211 }
212
213 # possibly set yrange
214 $yrange = "";
215 if( $yr ne "zzzzzzzzzzz" ){
216 @parts = split(',',$yr);
217 if( $#parts != 1 ){
218 print "Error: more than two fields in your -yr value\n";
219 exit;
220 }
221 $yrange = sprintf("set yrange [%f:%f]", $parts[0], $parts[1]);
222 }
223
224 @lines = ( "#!/bin/sh",
225 "gnuplot << EOF",
226 "reset",
227 "set style fill solid 1.00 noborder",
228 "set style histogram rowstacked",
229 "set style data histograms",
230 "set ylabel \"Bits x direction of regulation\"",
231 "set key outside",
232 "set xrange [$min: $max]",
233 "$tics",
234 "$keytoggle",
235 "$xtoggle",
236 "$ytoggle",
237 "$yrange",
238 "set terminal $format",
239 "set output \'$o\'",
240 "plot \'$name.logo\' u 1 notitle lc rgbcolor \"#000000\", \'\' u 2 notitle lc rgbcolor \"#008800\", \'\' u 3 notitle lc rgbcolor \"#00FF00\", \'\' u 7 t \"++\" lc rgbcolor \"#FF0000\", \'\' u 8 t \"+\" lc rgbcolor \"#880000\", \'\' u 9 t \"0\" lc rgbcolor \"#000000\", \'\' u 10 t \"-\" lc rgbcolor \"#008800\", \'\' u 11 t \"--\" lc rgbcolor \"#00FF00\", \'\' u 4 notitle lc rgbcolor \"#000000\", \'\' u 5 notitle lc rgbcolor \"#880000\", \'\' u 6 notitle lc rgbcolor \"#FF0000\"",
241 "EOF"
242 );
243
244 $command = sprintf("%s\n", $lines[0]);
245 for($i=1; $i<= $#lines; $i++){
246 $command = sprintf("%s%s\n", $command, $lines[$i]);
247 }
248
249 system("$command");
250
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