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7
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1 #!/usr/bin/perl
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2
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3 use strict;
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4 use Switch;
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5 use Getopt::Long;
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6 use lib ".";
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7
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8 my $usage = qq~Usage:$0 <args>
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9 where <args> are:
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10 -c, --count <SNP count SNiPloid output>
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11 -a, --annotation <annotation file in GFF3>
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12 -o, --output_png <output PNG file>
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13 -s, --scale <scale. Default:100000>
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14 -t, --type_analysis <type of analysis: polyploid_diploid or polyploid_polyploid. Default:polyploid_diploid>
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15 -m, --max_nb_chrom <maximum number of chromomsome to display. Default:20>
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16 -n, --nb_min_snp <minimal number of SNP to calculate ratio. Default:10>
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17 -d, --display_cat <display ratio for each category instead of intra-polyploid and inter-diploid (yes/no). Default:no>
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18 ~;
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19 $usage .= "\n";
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20
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21 my ($snp_count,$annotation,$output_png,$global_scale,$max_nb_chrom,$type_analysis);
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22
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23 my $global_scale = 10000;
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24 my $max_nb_chrom = 20;
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25 my $nb_min_snp = 10;
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26 my $display_cat = "no";
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27
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28
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29 GetOptions(
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30 "count=s" => \$snp_count,
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31 "annotation=s" => \$annotation,
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32 "output_png=s" => \$output_png,
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33 "scale=s" => \$global_scale,
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34 "max_nb_chrom=s" => \$max_nb_chrom,
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35 "type_analysis=s" => \$type_analysis,
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36 "nb_min_snp=s" => \$nb_min_snp,
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37 "display_cat=s" => \$display_cat
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38 );
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39
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40
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41 die $usage
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42 if ( !$snp_count || !$annotation || !$output_png || !$type_analysis);
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43
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44 my %proportions_categories;
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45 my %ratios;
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46 my %ratios_poly_diploid;
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47 my %nb_snps;
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48 open(my $COUNT,$snp_count);
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49 <$COUNT>;
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50 while(<$COUNT>)
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51 {
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52 my $line =$_;
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53 chomp($line);
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54 my @infos = split(/\t/,$line);
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55
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56
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57 if ($type_analysis eq "polyploid_diploid")
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58 {
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59 my $gene = $infos[0];
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60 my $nb_snp = $infos[2];
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61 my $nb_1 = $infos[3];
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62 my $nb_2 = $infos[4];
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63 my $nb_3or4 = $infos[5];
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64 my $nb_3 = $infos[6];
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65 my $nb_4 = $infos[7];
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66 my $nb_5 = $infos[8];
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67 my $nb_other = $infos[9];
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68 my $nb_heterozygot_diploid = $infos[10];
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69 my $nb_snp_diploid = $infos[11];
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70 my $nb_snp_polyploid = $infos[12];
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71
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72 $nb_snps{$gene} = $nb_snp;
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73 my $sum = $nb_1 + $nb_2 + $nb_3or4 + $nb_5 + $nb_3 + $nb_4 + $nb_other + $nb_heterozygot_diploid;
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74
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75 if ($nb_snp >= $nb_min_snp)
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76 {
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77 if ($nb_1)
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78 {
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79 $proportions_categories{$gene}{"1"} = $nb_1/$nb_snp;
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80 }
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81 if ($nb_2)
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82 {
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83 $proportions_categories{$gene}{"2"} = $nb_2/$nb_snp;
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84 }
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85 if ($nb_5)
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86 {
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87 $proportions_categories{$gene}{"5"} = $nb_5/$nb_snp;
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88 }
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89 if ($nb_3or4)
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90 {
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91 $proportions_categories{$gene}{"3or4"} = $nb_3or4/$nb_snp;
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92 }
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93 }
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94
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95 my $ratio_g1 = $infos[13];
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96 my $ratio_g2 = $infos[14];
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97
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98 if ($ratio_g1)
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99 {
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100 $ratios{$gene} = $ratio_g1;
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101 }
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102 }
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103
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104 if ($type_analysis eq "polyploid_polyploid")
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105 {
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106 my $gene = $infos[0];
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107 my $nb_snp = $infos[2];
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108 my $nb_equal = $infos[3] + $infos[4];
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109 my $nb_diff = $infos[7];
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110 $nb_snps{$gene} = $nb_snp;
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111 if ($nb_snp >= $nb_min_snp)
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112 {
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113 if ($nb_equal)
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114 {
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115 $proportions_categories{$gene}{"equal"} = $nb_equal/$nb_snp;
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116 }
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117 if ($nb_diff)
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118 {
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119 $proportions_categories{$gene}{"difference"} = $nb_diff/$nb_snp;
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120 }
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121 }
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122 }
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123
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124 }
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125 close($COUNT);
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126
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127
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128
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129
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130 my $max_pos = 0;
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131 my %chrom_sizes;
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132 my $chrom_particule;
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133 my %genes;
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134 my %gene_positions;
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135
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136 open(my $ANNOT,$annotation);
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137 while(<$ANNOT>)
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138 {
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139 my $line =$_;
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140 chomp($line);
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141 if (!/^#/ && /gene/)
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142 {
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143 my @infos = split(/\t/,$line);
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144 my $chrom = $infos[0];
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145 if ($chrom =~/^(\w+_)(\d+)$/)
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146 {
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147 $chrom_particule = $1;
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148 $chrom = $2;
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149 }
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150
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151 my $attributes = $infos[8];
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152 my $gene_name;
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153 if ($attributes =~/Name=([^;]+);/)
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154 {
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155 $gene_name = $1;
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156 }
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157 if (!$gene_name && $attributes =~/ID=([^;]+);/)
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158 {
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159 $gene_name = $1;
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160 }
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161 if ($gene_name =~/(.*)_G1/)
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162 {
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163 $gene_name = $1;
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164 }
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165 else
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166 {
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167 next;
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168 }
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169 if (not defined $nb_snps{$gene_name})
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170 {
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171 next;
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172 }
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173
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174 my $start = $infos[3];
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175 my $end = $infos[4];
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176 my $pos = sprintf("%.0f", ($start + (($end - $start) / 2)));
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177
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178 $end = $end / $global_scale;
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179 if ($chrom_sizes{$chrom})
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180 {
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181 if ($end > $chrom_sizes{$chrom})
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182 {
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183 $chrom_sizes{$chrom} = $end;
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184 if ($end > $max_pos)
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185 {
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186 $max_pos = $end;
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187 }
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188 }
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189 }
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190 else
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191 {
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192 $chrom_sizes{$chrom} = $end;
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193 if ($end > $max_pos)
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194 {
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195 $max_pos = $end;
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196 }
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197 }
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198 $genes{$gene_name} = "$chrom:$pos";
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199 $gene_positions{$chrom}{$pos}= $gene_name;
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200 }
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201 }
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202 close($ANNOT);
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203
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204
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205
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206 use GD;
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207 use GD::Simple;
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208 use GD::Image;
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209
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210
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211
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212
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213 ####################
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214 # drawing
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215 ####################
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216
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217 my $scale = 800 / $max_pos;
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218
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219 my $margin_left = 80;
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220 my $margin_right = 50;
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221 my $margin_top = 50;
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222 my $margin_legend = 100;
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223 my $margin_bottom = 10;
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224 my $margin_between_chromosomes = 25;
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225 my $margin_between_section = 50;
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226 my $chrom_width = 10;
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227 my $gene_width = 1;
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228
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229 my $nb_group = 1;
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230
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231 my $width_of_picture = scalar keys(%gene_positions);
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232 if (scalar keys(%gene_positions) > $max_nb_chrom)
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233 {
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234 $width_of_picture = $max_nb_chrom;
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235 }
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236
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237 my $diagram_img = GD::Simple->new(($margin_left + $margin_right + ($max_pos*$scale)),
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238 ($margin_top + ((($chrom_width * $nb_group) + ($margin_between_chromosomes * ($nb_group-1))) * $width_of_picture) + ($margin_between_section * $width_of_picture) + $margin_bottom + $margin_legend)
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239 );
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240
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241 my $yellow = $diagram_img->colorAllocate(247,254,46);
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242 my $orange_light = $diagram_img->colorAllocate(250,204,46);
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243 my $red_light = $diagram_img->colorAllocate(254,100,46);
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244 my $red = $diagram_img->colorAllocate(254,46,46);
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245 my $orange = $diagram_img->colorAllocate(254,154,46);
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246
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247
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248 # draw chromosomes
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249 my $num_chrom = 0;
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250 my @sorted_chrom = sort {$a <=> $b} keys(%gene_positions);
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251
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252 my $nombre_genes = 0;
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253 my $y_end;
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254 foreach my $chrom(@sorted_chrom)
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255 {
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256 if (!$chrom)
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257 {
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258 next;
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259 }
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260
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261 if ($num_chrom > ($max_nb_chrom - 1))
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262 {
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263 last;
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264 }
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265 my $ref_hash = $gene_positions{$chrom};
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266 my %hash = %$ref_hash;
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267
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268 my $section_size = $chrom_width + (($margin_between_chromosomes + $chrom_width) * ($nb_group - 1));
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269
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270 # draw chromosome (X number of groups)
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271
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272 $diagram_img->fgcolor('black');
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273 $diagram_img->bgcolor('white');
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274 $diagram_img->setThickness(1);
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275 my $chrom_chain = $chrom_particule . $chrom;
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276
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277 $diagram_img->rectangle( $margin_left,
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278 $margin_top + (($section_size + $margin_between_section) * $num_chrom),
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279 $margin_left + ($chrom_sizes{$chrom}*$scale),
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280 $margin_top + $chrom_width + (($section_size + $margin_between_section) * $num_chrom)
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281 );
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282
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283 $diagram_img->fgcolor('black');
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284 $diagram_img->moveTo(5,$margin_top + $chrom_width + (($section_size + $margin_between_section) * $num_chrom) - 1);
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285 $y_end = $margin_top + $chrom_width + (($section_size + $margin_between_section) * ($num_chrom+1)) - 1;
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286 $diagram_img->fontsize(12);
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287 $diagram_img->font('Times');
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288 $diagram_img->string($chrom_particule . $chrom);
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289
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290
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291 my $previous_x_5;
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292 my $previous_x_1;
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293 my $previous_x_2;
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294 my $previous_x_3or4;
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295 my $previous_y_5;
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296 my $previous_y_1;
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297 my $previous_y_2;
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298 my $previous_y_3or4;
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299
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300 my $previous_x_equal;
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301 my $previous_x_diff;
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302 my $previous_y_equal;
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303 my $previous_y_diff;
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304
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305 my $previous_x_snp_diplo;
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306 my $previous_x_snp_poly;
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307 my $previous_y_snp_diplo;
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308 my $previous_y_snp_poly;
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309
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310 my $previous_x_ratio_diplo_poly;
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311 my $previous_y_ratio_diplo_poly;
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312
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313 # draw genes
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314 foreach my $pos(sort{$a <=> $b}keys(%hash))
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315 {
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316 my $gene = $gene_positions{$chrom}{$pos};
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317 if (not defined $nb_snps{$gene} or $nb_snps{$gene} < $nb_min_snp)
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318 {
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319 next;
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320 }
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321
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322 if ($type_analysis eq "polyploid_diploid")
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323 {
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324 #####################################################
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325 # draw ratio (subgenomic contribution)
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326 #####################################################
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327 my $color = "gray";
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328 if ($ratios{$gene})
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329 {
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330 my $ratio_g1 = $ratios{$gene};
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331 if ($ratio_g1 <= 30)
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332 {
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333 $color = $red;
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334 }
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335 elsif ($ratio_g1 > 30 && $ratio_g1 <= 40)
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336 {
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337 $color = $red_light;
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338 }
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339 elsif ($ratio_g1 > 40 && $ratio_g1 <= 60)
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340 {
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341 $color = $orange;
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342 }
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343 elsif ($ratio_g1 > 60 && $ratio_g1 <= 70)
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344 {
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345 $color = $orange_light;
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346 }
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347 elsif ($ratio_g1 > 70)
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348 {
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349 $color = $yellow;
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350 }
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351 }
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352
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353 $pos = $pos / $global_scale;
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354
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355 $diagram_img->fgcolor($color);
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356 $diagram_img->bgcolor($color);
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357 $diagram_img->rectangle( $margin_left + ($pos*$scale) - ($gene_width / 2),
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358 $margin_top + (($section_size + $margin_between_section) * $num_chrom) + 1,
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359 $margin_left + ($pos*$scale) + ($gene_width / 2),
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360 $margin_top + $chrom_width + (($section_size + $margin_between_section) * $num_chrom) - 1
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361 );
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362
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363
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364
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365 #####################################################
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366 # draw SNP categories
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367 #####################################################
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368
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369 my $proportion_5 = $proportions_categories{$gene}{"5"};
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370 my $proportion_1 = $proportions_categories{$gene}{"1"};
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371 my $proportion_2 = $proportions_categories{$gene}{"2"};
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372 my $proportion_3or4 = $proportions_categories{$gene}{"3or4"};
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373 my $ratio_poly_diplo = $ratios_poly_diploid{$gene};
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374
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375 my $draw = 0;
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376 if (defined $previous_x_5)
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377 {
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378 $draw = 1;
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379 }
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380
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381
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382 #######################
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383 # SNP category 5
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384 #######################
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385 if ($draw)
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386 {
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387 $diagram_img->moveTo($previous_x_5,$previous_y_5);
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388 }
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389 $previous_x_5 = $margin_left + ($pos*$scale) - 1;
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390 $diagram_img->setThickness(2);
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391 $diagram_img->fgcolor("red");
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392 $diagram_img->bgcolor("red");
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393 $previous_y_5 = $margin_top + (($section_size + $margin_between_section) * $num_chrom) + 1 - ($proportion_5 * 20) - 7;
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394 if ($draw)
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395 {
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396 $diagram_img->lineTo($previous_x_5,$previous_y_5);
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397 }
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398
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399 if ($display_cat eq "yes")
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400 {
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401 #######################
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402 # SNP category 1
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403 #######################
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404 if ($draw)
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405 {
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406 $diagram_img->moveTo($previous_x_1,$previous_y_1);
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407 }
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408 $previous_x_1 = $margin_left + ($pos*$scale) - 1;
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409 $diagram_img->fgcolor("orange");
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410 $diagram_img->bgcolor("orange");
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411 $previous_y_1 = $margin_top + (($section_size + $margin_between_section) * $num_chrom) + 1 - ($proportion_1 * 20) - 7;
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412 if ($draw)
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413 {
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|
|
414 $diagram_img->lineTo($previous_x_1,$previous_y_1);
|
|
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415 }
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416
|
|
|
417
|
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|
418 #######################
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419 # SNP category 2
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|
420 #######################
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421 if ($draw)
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422 {
|
|
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423 $diagram_img->moveTo($previous_x_2,$previous_y_2);
|
|
|
424 }
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|
|
425 $previous_x_2 = $margin_left + ($pos*$scale) - 1;
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426 $diagram_img->fgcolor("purple");
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|
|
427 $diagram_img->bgcolor("purple");
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|
|
428 $previous_y_2 = $margin_top + (($section_size + $margin_between_section) * $num_chrom) + 1 - ($proportion_2 * 20) - 7;
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|
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429 if ($draw)
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|
|
430 {
|
|
|
431 $diagram_img->lineTo($previous_x_2,$previous_y_2);
|
|
|
432 }
|
|
|
433
|
|
|
434
|
|
|
435 #######################
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|
|
436 # SNP category 3 or 4
|
|
|
437 #######################
|
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|
438 if ($draw)
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|
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439 {
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|
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440 $diagram_img->moveTo($previous_x_3or4,$previous_y_3or4);
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|
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441 }
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|
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442 $previous_x_3or4 = $margin_left + ($pos*$scale) - 1;
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|
|
443 $diagram_img->fgcolor("green");
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|
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444 $diagram_img->bgcolor("green");
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|
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445 $previous_y_3or4 = $margin_top + (($section_size + $margin_between_section) * $num_chrom) + 1 - ($proportion_3or4 * 20) - 7;
|
|
|
446 if ($draw)
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|
|
447 {
|
|
|
448 $diagram_img->lineTo($previous_x_3or4,$previous_y_3or4);
|
|
|
449 }
|
|
|
450 }
|
|
|
451
|
|
|
452 }
|
|
|
453
|
|
|
454 if ($type_analysis eq "polyploid_polyploid")
|
|
|
455 {
|
|
|
456 my $color = "gray";
|
|
|
457 $pos = $pos / $global_scale;
|
|
|
458
|
|
|
459 $diagram_img->fgcolor($color);
|
|
|
460 $diagram_img->bgcolor($color);
|
|
|
461 $diagram_img->rectangle( $margin_left + ($pos*$scale) - ($gene_width / 2),
|
|
|
462 $margin_top + (($section_size + $margin_between_section) * $num_chrom) + 1,
|
|
|
463 $margin_left + ($pos*$scale) + ($gene_width / 2),
|
|
|
464 $margin_top + $chrom_width + (($section_size + $margin_between_section) * $num_chrom) - 1
|
|
|
465 );
|
|
|
466
|
|
|
467
|
|
|
468
|
|
|
469 my $proportion_equal = $proportions_categories{$gene}{"equal"};
|
|
|
470 my $proportion_diff = $proportions_categories{$gene}{"difference"};
|
|
|
471
|
|
|
472 my $draw = 0;
|
|
|
473 if (defined $previous_x_equal)
|
|
|
474 {
|
|
|
475 $draw = 1;
|
|
|
476 }
|
|
|
477
|
|
|
478
|
|
|
479 ##################################################
|
|
|
480 # SNP category : equality between 2 polyploids
|
|
|
481 ##################################################
|
|
|
482 if ($draw)
|
|
|
483 {
|
|
|
484 $diagram_img->moveTo($previous_x_equal,$previous_y_equal);
|
|
|
485 }
|
|
|
486 $previous_x_equal = $margin_left + ($pos*$scale) - 1;
|
|
|
487 $diagram_img->setThickness(2);
|
|
|
488 $diagram_img->fgcolor("red");
|
|
|
489 $diagram_img->bgcolor("red");
|
|
|
490 $previous_y_equal = $margin_top + (($section_size + $margin_between_section) * $num_chrom) + 1 - ($proportion_equal * 20) - 7;
|
|
|
491 if ($draw)
|
|
|
492 {
|
|
|
493 $diagram_img->lineTo($previous_x_equal,$previous_y_equal);
|
|
|
494 }
|
|
|
495 }
|
|
|
496
|
|
|
497 $nombre_genes++;
|
|
|
498 }
|
|
|
499
|
|
|
500 $num_chrom++;
|
|
|
501 }
|
|
|
502
|
|
|
503 if ($type_analysis eq "polyploid_polyploid")
|
|
|
504 {
|
|
|
505 $diagram_img->moveTo(5,$y_end);
|
|
|
506 $diagram_img->setThickness(2);
|
|
|
507 $diagram_img->fgcolor("red");
|
|
|
508 $diagram_img->bgcolor("red");
|
|
|
509 $diagram_img->lineTo(25,$y_end);
|
|
|
510 $diagram_img->fgcolor("black");
|
|
|
511 $diagram_img->moveTo(30,$y_end + 5);
|
|
|
512 $diagram_img->fontsize(12);
|
|
|
513 $diagram_img->font('Times');
|
|
|
514 $diagram_img->string("% SNP where P1 = P2");
|
|
|
515 }
|
|
|
516 elsif ($type_analysis eq "polyploid_diploid")
|
|
|
517 {
|
|
|
518 if ($display_cat eq "yes")
|
|
|
519 {
|
|
|
520 $diagram_img->moveTo(5,$y_end);
|
|
|
521 $diagram_img->setThickness(2);
|
|
|
522 $diagram_img->fgcolor("orange");
|
|
|
523 $diagram_img->bgcolor("orange");
|
|
|
524 $diagram_img->lineTo(25,$y_end);
|
|
|
525 $diagram_img->fgcolor("black");
|
|
|
526 $diagram_img->moveTo(30,$y_end + 5);
|
|
|
527 $diagram_img->fontsize(12);
|
|
|
528 $diagram_img->font('Times');
|
|
|
529 $diagram_img->string("% SNP type 1");
|
|
|
530
|
|
|
531 $diagram_img->moveTo(5,$y_end + 20);
|
|
|
532 $diagram_img->setThickness(2);
|
|
|
533 $diagram_img->fgcolor("purple");
|
|
|
534 $diagram_img->bgcolor("purple");
|
|
|
535 $diagram_img->lineTo(25,$y_end + 20);
|
|
|
536 $diagram_img->fgcolor("black");
|
|
|
537 $diagram_img->moveTo(30,$y_end + 25);
|
|
|
538 $diagram_img->fontsize(12);
|
|
|
539 $diagram_img->font('Times');
|
|
|
540 $diagram_img->string("% SNP type 2");
|
|
|
541
|
|
|
542 $diagram_img->moveTo(5,$y_end + 40);
|
|
|
543 $diagram_img->setThickness(2);
|
|
|
544 $diagram_img->fgcolor("green");
|
|
|
545 $diagram_img->bgcolor("green");
|
|
|
546 $diagram_img->lineTo(25,$y_end + 40);
|
|
|
547 $diagram_img->fgcolor("black");
|
|
|
548 $diagram_img->moveTo(30,$y_end + 45);
|
|
|
549 $diagram_img->fontsize(12);
|
|
|
550 $diagram_img->font('Times');
|
|
|
551 $diagram_img->string("% SNP type 3 or 4");
|
|
|
552
|
|
|
553 $diagram_img->moveTo(5,$y_end + 60);
|
|
|
554 $diagram_img->setThickness(2);
|
|
|
555 $diagram_img->fgcolor("red");
|
|
|
556 $diagram_img->bgcolor("red");
|
|
|
557 $diagram_img->lineTo(25,$y_end + 60);
|
|
|
558 $diagram_img->fgcolor("black");
|
|
|
559 $diagram_img->moveTo(30,$y_end + 65);
|
|
|
560 $diagram_img->fontsize(12);
|
|
|
561 $diagram_img->font('Times');
|
|
|
562 $diagram_img->string("% SNP type 5");
|
|
|
563 }
|
|
|
564 else
|
|
|
565 {
|
|
|
566 $diagram_img->moveTo(5,$y_end);
|
|
|
567 $diagram_img->setThickness(2);
|
|
|
568 $diagram_img->fgcolor("red");
|
|
|
569 $diagram_img->bgcolor("red");
|
|
|
570 $diagram_img->lineTo(25,$y_end);
|
|
|
571 $diagram_img->fgcolor("black");
|
|
|
572 $diagram_img->moveTo(30,$y_end + 5);
|
|
|
573 $diagram_img->fontsize(12);
|
|
|
574 $diagram_img->font('Times');
|
|
|
575 $diagram_img->string("% SNP Class 5 per gene (SNP Intra-Diploids = SNP Intra-Polyploid)");
|
|
|
576 }
|
|
|
577
|
|
|
578 $diagram_img->moveTo(5,$y_end + 30);
|
|
|
579 $diagram_img->fontsize(12);
|
|
|
580 $diagram_img->font('Times');
|
|
|
581 $diagram_img->string("Estimate of subgenomic contribution to the transcriptome for each gene (%G2)");
|
|
|
582
|
|
|
583
|
|
|
584 $diagram_img->moveTo(25,$y_end + 45);
|
|
|
585 $diagram_img->setThickness(10);
|
|
|
586 $diagram_img->fgcolor($red);
|
|
|
587 $diagram_img->bgcolor($red);
|
|
|
588 $diagram_img->lineTo(30,$y_end + 45);
|
|
|
589 $diagram_img->fgcolor("black");
|
|
|
590 $diagram_img->moveTo(35,$y_end + 50);
|
|
|
591 $diagram_img->fontsize(12);
|
|
|
592 $diagram_img->font('Times');
|
|
|
593 $diagram_img->string("0-30%");
|
|
|
594
|
|
|
595 $diagram_img->moveTo(95,$y_end + 45);
|
|
|
596 $diagram_img->setThickness(10);
|
|
|
597 $diagram_img->fgcolor($red_light);
|
|
|
598 $diagram_img->bgcolor($red_light);
|
|
|
599 $diagram_img->lineTo(100,$y_end + 45);
|
|
|
600 $diagram_img->fgcolor("black");
|
|
|
601 $diagram_img->moveTo(105,$y_end + 50);
|
|
|
602 $diagram_img->fontsize(12);
|
|
|
603 $diagram_img->font('Times');
|
|
|
604 $diagram_img->string("30-40%");
|
|
|
605
|
|
|
606 $diagram_img->moveTo(165,$y_end + 45);
|
|
|
607 $diagram_img->setThickness(10);
|
|
|
608 $diagram_img->fgcolor($orange);
|
|
|
609 $diagram_img->bgcolor($orange);
|
|
|
610 $diagram_img->lineTo(170,$y_end + 45);
|
|
|
611 $diagram_img->fgcolor("black");
|
|
|
612 $diagram_img->moveTo(175,$y_end + 50);
|
|
|
613 $diagram_img->fontsize(12);
|
|
|
614 $diagram_img->font('Times');
|
|
|
615 $diagram_img->string("40-60%");
|
|
|
616
|
|
|
617 $diagram_img->moveTo(235,$y_end + 45);
|
|
|
618 $diagram_img->setThickness(10);
|
|
|
619 $diagram_img->fgcolor($orange_light);
|
|
|
620 $diagram_img->bgcolor($orange_light);
|
|
|
621 $diagram_img->lineTo(240,$y_end + 45);
|
|
|
622 $diagram_img->fgcolor("black");
|
|
|
623 $diagram_img->moveTo(245,$y_end + 50);
|
|
|
624 $diagram_img->fontsize(12);
|
|
|
625 $diagram_img->font('Times');
|
|
|
626 $diagram_img->string("60-70%");
|
|
|
627
|
|
|
628 $diagram_img->moveTo(305,$y_end + 45);
|
|
|
629 $diagram_img->setThickness(10);
|
|
|
630 $diagram_img->fgcolor($yellow);
|
|
|
631 $diagram_img->bgcolor($yellow);
|
|
|
632 $diagram_img->lineTo(310,$y_end + 45);
|
|
|
633 $diagram_img->fgcolor("black");
|
|
|
634 $diagram_img->moveTo(315,$y_end + 50);
|
|
|
635 $diagram_img->fontsize(12);
|
|
|
636 $diagram_img->font('Times');
|
|
|
637 $diagram_img->string("70-100%");
|
|
|
638
|
|
|
639 $diagram_img->moveTo(25,$y_end + 60);
|
|
|
640 $diagram_img->setThickness(10);
|
|
|
641 $diagram_img->fgcolor("gray");
|
|
|
642 $diagram_img->bgcolor("gray");
|
|
|
643 $diagram_img->lineTo(30,$y_end + 60);
|
|
|
644 $diagram_img->fgcolor("black");
|
|
|
645 $diagram_img->moveTo(35,$y_end + 65);
|
|
|
646 $diagram_img->fontsize(12);
|
|
|
647 $diagram_img->font('Times');
|
|
|
648 $diagram_img->string("No ratio information, no SNP class 5 in this gene");
|
|
|
649
|
|
|
650 }
|
|
|
651
|
|
|
652
|
|
|
653 open( DIAGRAM_PICT, ">$output_png" );
|
|
|
654 binmode(DIAGRAM_PICT);
|
|
|
655 print DIAGRAM_PICT $diagram_img->png;
|
|
|
656 close DIAGRAM_PICT;
|
