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1 #!/usr/bin/perl
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2 # make a logo-ish gnu-plottable representation of a score matrix
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3
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4 use Getopt::Long;
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5
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6 #
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7 # command line arguments
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8 #
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9 $options = "Usage: ./Make_Logo.pl <OPTIONS>
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10 -m .model file from EMBER (required)
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11 -c comparison list (used to make labels for the x-axis)
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12 -o output (required)
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13 -a include comparisons not used by EMBER (preceded by # in the .model file: y or n, default n)
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14 -f image file format (default 1)
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15 1 - eps
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16 2 - cgm
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17 -k key on/off (y or n, default y)
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18 -lx x labels on/off (y or n, default y)
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19 -ly y labels on/off (y or n, default y)
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20 -yr set yrange manually (enter <min>,<max>, e.g. -1.5,3.5; default chosen automatically)
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21 \n";
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22
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23 $m = "";
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24 $c = "";
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25 $o = "";
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26 $a = "n";
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27 $f = 1;
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28 $k = "y";
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29 $lx= "y";
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30 $ly= "y";
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31 $yr= "zzzzzzzzzzz";
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32
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33 GetOptions('m=s' => \$m,
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34 'c=s' => \$c,
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35 'o=s' => \$o,
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36 'a=s' => \$a,
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37 'f=i' => \$f,
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38 'k=s' => \$k,
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39 'lx=s'=> \$lx,
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40 'ly=s'=> \$ly,
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41 'yr=s'=> \$yr
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42 ) || die "\n$options";
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43
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44 if( $m eq "" ){
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45 print "Error: set a value for -m\n\n$options";
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46 exit;
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47 }
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48 if( $o eq "" ){
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49 print "Error: set a value for -o\n\n$options";
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50 exit;
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51 }
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52 if( $f != 1 && $f != 2 ){
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53 print "Error: set -f to be 1 or 2\n\n$options";
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54 exit;
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55 }
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56 if( $a ne "y" && $a ne "n" ){
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57 print "Error: set -a to be y or n\n\n$options";
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58 exit;
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59 }
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60 if( $k ne "y" && $k ne "n" ){
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61 print "Error: set -k to be y or n\n\n$options";
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62 exit;
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63 }
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64 if( $lx ne "y" && $lx ne "n" ){
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65 print "Error: set -lx to be y or n\n\n$options";
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66 exit;
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67 }
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68 if( $ly ne "y" && $ly ne "n" ){
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69 print "Error: set -ly to be y or n\n\n$options";
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70 exit;
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71 }
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72 if( $yr ne "zzzzzzzzzzz" && $yr !~ /,/ ){
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73 print "Error: if setting -yr, choose a range delimited by a comma\n\n$options";
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74 exit;
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75 }
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76
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77 @parts = split('\.',$m);
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78 $name = $o;
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79 #for($i=1; $i< $#parts; $i++){
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80 # $name = sprintf("%s.%s", $name, $parts[$i]);
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81 #}
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82
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83 #
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84 # read in matrix
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85 #
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86 open(IN,"$m") || die "Error: can't open file $m\n";
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87 @re = ();
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88 @mat = ();
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89
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90 # burn 2 lines
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91 $line = <IN>;
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92 $line = <IN>;
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93
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94 @coloffs = ();
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95 while($line = <IN>){
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96 chomp($line);
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97 @parts = split(' ',$line);
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98 if( ($a eq "n" && $parts[0] !~ /#/) || $a eq "y" ){
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99 push(@coloffs, 1 );
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100 ($ind, $reval) = split(',', $parts[0]);
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101 if( $reval eq "nan" ){$reval = 0.0;}
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102 push(@re, $reval);
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103 @tmp = ();
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104 for($i=1; $i<= $#parts; $i++){
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105 if( $parts[$i] eq "NA" ){
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106 $parts[$i] = 0.0;
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107 }
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108 push(@tmp, $parts[$i]);
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109 }
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110 push(@mat, [@tmp] );
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111 }
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112 else{
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113 push(@coloffs, 0);
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114 }
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115 }
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116 close(IN);
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117
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118 #
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119 # rescale matrix so it's between 0 and 1, then multiply by re
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120 #
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121 for($i=0; $i<= $#mat; $i++){
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122 $min = $mat[$i][0];
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123 $max = $mat[$i][0];
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124 for($j=1; $j< 5; $j++){
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125 if( $min > $mat[$i][$j] ){ $min = $mat[$i][$j]; }
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126 if( $max < $mat[$i][$j] ){ $max = $mat[$i][$j]; }
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127 }
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128 for($j=0; $j< 5; $j++){
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129 if( $max != $min ){
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130 $mat[$i][$j] = $re[$i]*(($mat[$i][$j]-$min)/($max-$min));
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131 }
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132 else{
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133 $mat[$i][$j] = 0;
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134 }
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135 }
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136 }
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137
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138
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139 #
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140 # print out in stacked format
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141 #
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142 open(OUT,">$name.logo");
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143 for($i=0; $i<= $#mat; $i++){
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144 $posn = ($mat[$i][0] + $mat[$i][1] + 0.5*$mat[$i][2]);
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145 printf OUT ("%f ", -0.5*$mat[$i][2]);
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146 printf OUT ("%f ", -$mat[$i][3]);
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147 printf OUT ("%f ", -$mat[$i][4]);
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148 printf OUT ("%f ", 0.5*$mat[$i][2]);
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149 printf OUT ("%f ", $mat[$i][1]);
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150 printf OUT ("%f ", $mat[$i][0]);
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151 printf OUT ("0 0 0 0 0\n");
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152 }
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153 close(OUT);
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154
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155 #
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156 # make gnu-plotable file
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157 #
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158
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159 # possibly read in conditions to define xtics
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160 $tics = "";
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161 if( $c ne "" ){
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162 open(IN,"$c") || die "Error: can't open file $c\n";
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163 @comps = ();
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164 $i = 0;
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165 while($line = <IN>){
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166 chomp($line);
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167 @parts = split(' ',$line);
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168 if( $#parts != 1 ){
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169 print "Error: comparisons list does not have 2 columns\n";
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170 exit;
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171 }
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172 if( $coloffs[$i] == 1 ){
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173 $val = sprintf("%s vs %s", $parts[0], $parts[1]);
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174 push(@comps, $val);
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175 }
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176 $i++;
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177 }
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178 $tics = "set xtics(\"$comps[0]\" 0";
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179 for($i=1; $i<= $#comps; $i++){
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180 $tics = sprintf("%s, \"%s\" %i", $tics, $comps[$i], $i);
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181 }
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182 $tics = sprintf("%s)\nset xtics rotate by -45", $tics);
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183 }
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184
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185 # choose format
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186 if( $f == 1 ){
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187 $format = "postscript eps color 24";
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188 $suff = "eps";
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189 }
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190 if( $f == 2 ){
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191 $format = "cgm \"Helvetica\" 14";
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192 $suff = "cgm";
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193 }
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194
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195 # set xrange min and max
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196 $min = -0.5;
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197 $max = $#mat+0.5;
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198
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199 # possibly turn off key, xlabel, ylabel
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200 $keytoggle = "";
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201 $xtoggle = "";
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202 $ytoggle = "";
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203 if( $k eq "n" ){
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204 $keytoggle = "unset key";
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205 }
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206 if( $lx eq "n" ){
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207 $xtoggle = "unset xtics";
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208 }
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209 if( $ly eq "n" ){
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210 $ytoggle = "unset ylabel";
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211 }
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212
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213 # possibly set yrange
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214 $yrange = "";
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215 if( $yr ne "zzzzzzzzzzz" ){
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216 @parts = split(',',$yr);
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217 if( $#parts != 1 ){
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218 print "Error: more than two fields in your -yr value\n";
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219 exit;
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220 }
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221 $yrange = sprintf("set yrange [%f:%f]", $parts[0], $parts[1]);
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222 }
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223
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224 @lines = ( "#!/bin/sh",
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225 "gnuplot << EOF",
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226 "reset",
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227 "set style fill solid 1.00 noborder",
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228 "set style histogram rowstacked",
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229 "set style data histograms",
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230 "set ylabel \"Bits x direction of regulation\"",
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231 "set key outside",
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232 "set xrange [$min: $max]",
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233 "$tics",
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234 "$keytoggle",
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235 "$xtoggle",
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236 "$ytoggle",
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237 "$yrange",
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238 "set terminal $format",
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239 "set output \'$o\'",
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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\"",
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241 "EOF"
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242 );
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243
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244 $command = sprintf("%s\n", $lines[0]);
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245 for($i=1; $i<= $#lines; $i++){
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246 $command = sprintf("%s%s\n", $command, $lines[$i]);
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247 }
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248
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249 system("$command");
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250
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251
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252
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253
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254
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