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plot.genome.featureCluster.pl
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#!/usr/bin/env perl -w
use Getopt::Long;
my ($list,$prefix,$outdir,$conf);
GetOptions("list:s"=>\$list,
"prefix:s"=>\$prefix,
"outdir:s"=>\$outdir,
"conf:s"=>\$conf
);
die "
perl $0 [options]:
* --list <str> two formats: [sample gff genome seq_id1 seq_draw_start1 seq_draw_end1 genome seq_id2 seq_draw_start2 seq_draw_end2 ...]
or [sample gff genome]no seq_id mean full length of whole gff
* --prefix <str>
* --outdir <str>
* --conf <str>
writed by myth
" unless($list && $prefix && $outdir && $conf);
if(! -d "$outdir"){
`mkdir -p $outdir`;
}
my %conf = &read_conf($conf);
%conf = &default_setting(%conf);
#&display_conf(%conf);
my $shift_angle_closed_feature=0;
my ($svg_width,$svg_height) = split(',',$conf{'svg_width_height'});
## position of features for crosslink
my %positon_links;
my @fetures_links;
##start:get max scaffolds lengths in gff file
my $max_length;
my ($ref_name_width_ratio, $cluster_width_ratio, $legend_width_ratio) = split(/-/, $conf{width_ratio_ref_cluster_legend});
if($ref_name_width_ratio+$cluster_width_ratio+$legend_width_ratio !=1){
die "error:width_ratio_ref_cluster_legend in $list ,the sum is not equal to 1\n";
}
my $space_len = $conf{space_between_blocks};# 500bp是默认的blocks之间的间距
##
###start:get scaffold length in genome file and scaffold length in gff file of list
my ($genome, $gff, $sample_num) = &read_list($list);
my %genome=%$genome;
my %gff=%$gff;
my $ends_extend_ratio = 0.1;
foreach my $s(sort {$gff{$b}{chooselen_all}<=>$gff{$a}{chooselen_all}} keys %gff){
$max_length=$gff{$s}{chooselen_all};
#print "sample is $s\n";
#print "xxxx is $max_length\n";
last;
}
print "max_length is $max_length,\n";
my $ratio=$cluster_width_ratio*$svg_width/$max_length;
#print "ratio $cluster_width_ratio*$svg_width/$max_length\n";
my $index;
my $common_size;
my $top_bottom_margin=$conf{top_bottom_margin};
my %orders;
my $svg="<svg xmlns=\"http://www.w3.org/2000/svg\" version=\"1.1\" width=\"$svg_width\" height=\"$svg_height\" >\n";
open LI,"$list" or die "$!";
my $top_distance=$top_bottom_margin/2*$svg_height;
my $sample_single_height = (1 - $top_bottom_margin)*$svg_height/$sample_num; # 每个track的高度
my $id_line_height = 0.05*$conf{genome_height_ratio}*2*$sample_single_height; # 每个block的genome的高度
my $left_distance_init = (1 + 0.1) * $ref_name_width_ratio * $svg_width ;#block左侧起点的x轴,0.1是指ref name和第一个block的间隔
while(<LI>){
chomp;
next if($_=~ /^#/ || $_=~ /^\s*$/);
$index++;
my ($sample,@tmp) = split(/\s+/,$_);
my $block_distance = $space_len*$ratio; # block_distance 是每个block的间距
my $flag;
my $left_distance = $left_distance_init ;#block左侧起点的x轴,0.1是指ref name和第一个block的间隔
#my $line_to_sample_single_top_dis=0.45; #track cluster顶部 y 轴在一个track高度的0.45，即cluster的y轴的底部在0.55，即一个cluster高度是整个track的0.55-0.45=0.1
my $line_to_sample_single_top_dis = 0.5 - 0.05*$conf{genome_height_ratio};#genome_height_ratio
my $shift_x = $left_distance;
# write sample name for track
my $text_size = $id_line_height * 1; # sample name 文字大小
$common_size = $text_size;
my $ref_name_x = $svg_width * $ref_name_width_ratio; # sample name 右下角end的x和y轴
my $ref_name_y = $top_distance + (0.5 + 0.05*$conf{genome_height_ratio}) * $sample_single_height; #和block的genome起点的y坐标+block的genome的高度
if(not exists $conf{sample_name_old2new}{$sample}{new_name}){
$conf{sample_name_old2new}{$sample}{new_name} = $sample;
$conf{sample_name_old2new}{$sample}{new_color} = $conf{sample_name_color_default};
$conf{sample_name_old2new}{$sample}{new_font_size} = $conf{sample_name_font_size_default};
}
$svg.="<text x=\"$ref_name_x\" y=\"$ref_name_y\" font-size=\"$conf{sample_name_old2new}{$sample}{new_font_size}px\" fill=\"$conf{sample_name_old2new}{$sample}{new_color}\" text-anchor='end'>$conf{sample_name_old2new}{$sample}{new_name}</text>\n"; # draw sample name
print "draw sample name $conf{sample_name_old2new}{$sample}{new_name}\n";
my $pre_block='';
foreach my $block_index(sort {$a<=>$b} keys %{$gff{$sample}{block}}){ # one block_index ---> one scaffold ---> one cluster of genes
#print "block_index is $block_index, sample is $sample\n";
$flag++;
my @scf = keys %{$gff{$sample}{block}{$block_index}};
my $id_line_x=$left_distance; # 每个block的genome的起点的x,y坐标
my $id_line_y=$top_distance + $line_to_sample_single_top_dis * $sample_single_height; # 每个block的genome的起点的x,y坐标
my $id_line_width=$gff{$sample}{chooselen_single}{$block_index}{len} * $ratio; # 每个block的genome的宽度
#print "chooselen_single is $sample $gff{$sample}{chooselen_single}{$block_index} * $ratio\n";
### draw main scaffold line track
#$svg.="<rect x=\"$id_line_x\" y=\"$id_line_y\" width=\"$id_line_width\" height=\"$id_line_height\" style=\"fill:$conf{track_color}\" />\n";
my $track_order=$conf{track_order};
foreach my $f(keys %{$conf{feature_setting}}){
next if ( (not exists $conf{feature_setting}{$f}{track_order}) || $conf{feature_setting}{$f}{scf_id} ne $scf[0] || $conf{feature_setting}{$f}{sample} ne $sample);
#print "$conf{feature_setting}{$f}{scf_id} ne $scf[0] || $conf{feature_setting}{$f}{sample} ne $sample\n";
#print "f is $f\n\n";
my $start_f=$conf{feature_setting}{$f}{start};
my $end_f=$conf{feature_setting}{$f}{end};
if($start_f>=$gff{$sample}{chooselen_single}{$block_index}{start} && $end_f<=$gff{$sample}{chooselen_single}{$block_index}{end}){
$track_order=$conf{feature_setting}{$f}{track_order};
#print "$conf{feature_setting}{$f}{track_order}, $conf{feature_setting}{$f}{scf_id} ne $scf[0] || $conf{feature_setting}{$f}{sample} ne $sample;track_order is $track_order;sample is $sample, scf is @scf\n\n\n";
}
}
$orders{$track_order}.="<g><title>$scf[0],$gff{$sample}{chooselen_single}{$block_index}{start},$gff{$sample}{chooselen_single}{$block_index}{end}</title><rect x=\"$id_line_x\" y=\"$id_line_y\" width=\"$id_line_width\" height=\"$id_line_height\" style=\"fill:$conf{track_color}\" /></g>\n";
## 判断相邻的block是否来自同一条scaffold
if($scf[0] eq $pre_block and $conf{connect_with_same_scaffold}=~ /yes/i){
my $pre_x = $id_line_x - $block_distance;
my $pre_y = $id_line_y + 0.5 * $id_line_height;
my $now_x = $pre_x + $block_distance * 0.99;
my $now_y = $pre_y;
#print "pre_block $pre_block $pre_x $pre_y $now_x $now_y\n";
my $stroke_dasharray=$conf{connect_stroke_dasharray};
my $stroke_width=$conf{connect_stroke_width};
my $stroke_color=$conf{connect_stroke_color};
$svg.="<g fill=\"none\" stroke=\"$stroke_color\" stroke-width=\"$stroke_width\"><path stroke-dasharray=\"$stroke_dasharray\" d=\"M$pre_x,$pre_y L$now_x,$now_y\" /></g>";
}
$left_distance+=($block_distance+$id_line_width); #每个block左侧起点的x坐标shift
$pre_block = $scf[0];
### draw genes
#print "here\n";
#print "scf is @scf,$sample,$block_index\n";
my $angle_flag=0;
my $pre_index_end=0;
my $pre_scf_id="";
foreach my $index(sort {$gff{$sample}{block}{$block_index}{$scf[0]}{$a}{start}<=>$gff{$sample}{block}{$block_index}{$scf[0]}{$b}{start}} keys %{$gff{$sample}{block}{$block_index}{$scf[0]}}){
#next if($index eq "len");
#print "here $sample $block_index $scf[0] $index\n";
my $gene_height_medium=$id_line_height*$conf{feature_height_ratio};
my $index_id = $gff{$sample}{block}{$block_index}{$scf[0]}{$index}{id};
die "die:index_id is $index_id,$sample $block_index $scf[0] $index\n" if(not $index_id);
my $index_start = $gff{$sample}{block}{$block_index}{$scf[0]}{$index}{start};
my $index_end = $gff{$sample}{block}{$block_index}{$scf[0]}{$index}{end};
my $index_strand = $gff{$sample}{block}{$block_index}{$scf[0]}{$index}{strand};
my $index_start_raw = $gff{$sample}{block}{$block_index}{$scf[0]}{$index}{start_raw};
my $index_end_raw = $gff{$sample}{block}{$block_index}{$scf[0]}{$index}{end_raw};
my $index_color = (exists $conf{feature_setting}{$index_id}{feature_color})? $conf{feature_setting}{$index_id}{feature_color}:$conf{feature_color};
my $display_feature_label=(exists $conf{feature_setting}{$index_id}{display_feature_label})? $conf{feature_setting}{$index_id}{display_feature_label}:$conf{display_feature_label};
my $feature_not_mark_label = ($display_feature_label=~ /^yes$/i or $display_feature_label=~ /,yes/i)? $index_id:"";
my $index_label_content = (exists $conf{feature_setting}{$index_id}{feature_label})? (($display_feature_label=~ /^yes$/ or $display_feature_label=~ /^yes,/)? $conf{feature_setting}{$index_id}{feature_label}:""):$feature_not_mark_label;
my $index_label_size = (exists $conf{feature_setting}{$index_id}{feature_label_size})? $conf{feature_setting}{$index_id}{feature_label_size}:$conf{feature_label_size};
$index_label_col = (exists $conf{feature_setting}{$index_id}{feature_label_color})? $conf{feature_setting}{$index_id}{feature_label_color}:$conf{feature_label_color};
$index_label_position = (exists $conf{feature_setting}{$index_id}{pos_feature_label})? $conf{feature_setting}{$index_id}{pos_feature_label}:$conf{pos_feature_label};
#print "$index_id\t$index_label_position\n";
$index_label_angle = (exists $conf{feature_setting}{$index_id}{label_rotate_angle})? $conf{feature_setting}{$index_id}{label_rotate_angle}:$conf{label_rotate_angle};
$gene_height_medium = $id_line_height * $conf{feature_setting}{$index_id}{feature_height_ratio} if(exists $conf{feature_setting}{$index_id}{feature_height_ratio});
#print "index_label_angle is $index_label_angle\n";
my $gene_height_top=($conf{feature_shape}=~ /arrow/)? $id_line_height*$conf{feature_arrow_sharp_extent}:0;
my $sharp_len=($conf{ignore_sharp_arrow}=~ /yes/)? 0:$gene_height_top;
$conf{feature_setting}{$index_id}{cross_link_shift_y}=0.5*$gene_height_medium + $sharp_len;
my $gene_width_arrow=$conf{feature_arrow_width_extent};
$gene_width_arrow=$conf{feature_setting}{$index_id}{feature_arrow_width_extent} if(exists $conf{feature_setting}{$index_id}{feature_arrow_width_extent});
#print "$index_id gene_width_arrow is $gene_width_arrow\n";
$gene_height_top=$id_line_height*$conf{feature_setting}{$index_id}{feature_arrow_sharp_extent} if(exists $conf{feature_setting}{$index_id}{feature_arrow_sharp_extent});
my $feature_shift_y=($conf{feature_setting}{$index_id}{feature_shift_y})? $conf{feature_setting}{$index_id}{feature_shift_y}:$conf{feature_shift_y};
if($scf[0] eq $pre_scf_id && ($index_start - $pre_index_end) <= $conf{distance_closed_feature} && ($index_end - $index_start)< 300 ){
$angle_flag = 1
}
#print "angle is $angle_flag\n";
## draw_gene 函数需要重写，输入起点的xy坐标，正负链等信息即可
$svg.=&draw_genes(
$index_id,
$index_start,
$index_end,
$index_strand,
$index_start_raw,
$index_end_raw,
$gene_height_medium,
$gene_height_top,
$gene_width_arrow,
$shift_x,
$top_distance,
$feature_shift_y,
$sample_single_height,
$sample,
$scf[0],
$index_color,
$index_label_content,
$index_label_size,
$index_label_col,
$index_label_position,
$index_label_angle,
$angle_flag); ## draw_gene 函数需要重写，输入起点的xy坐标，正负链等信息即可
$pre_index_end = $index_end;
$pre_scf_id = $scf[0];
#print "sampe is $sample,id is $id;index is $index;$gff{$sample}{id}{$id}{$index}{start},$gff{$sample}{id}{$id}{$index}{end},$gff{$sample}{id}{$id}{$index}{strand},$gene_height_medium,$gene_height_top,$gene_width_arrow,$shift_x,$top_distance,$sample_single_height\n";
}
$shift_x+=($id_line_width+$block_distance);
}
$top_distance+=$sample_single_height;
#$gff{$sample}{id}{$arr[0]}{$gene_index}{end}=$arr[4]
}
close LI;
# draw crossing_links for feature crosslink
foreach my $pair(keys %{$conf{crossing_link}{index}}){
#$conf{crossing_link}{index}{"$arr[0],$arr[1]"}{$arr[2]} = $arr[3];
my ($up_id, $down_id) = split(",", $pair);
my $color=(exists $conf{crossing_link}{index}{$pair}{cross_link_color})? $conf{crossing_link}{index}{$pair}{cross_link_color}:$conf{cross_link_color};
my $cross_link_opacity=(exists $conf{crossing_link}{index}{$pair}{cross_link_opacity})? $conf{crossing_link}{index}{$pair}{cross_link_opacity}:$conf{cross_link_opacity};
my $cross_link_order=(exists $conf{crossing_link}{index}{$pair}{cross_link_order})? $conf{crossing_link}{index}{$pair}{cross_link_order}:$conf{cross_link_order};
my $cross_link_anchor_pos=(exists $conf{crossing_link}{index}{$pair}{cross_link_anchor_pos})? $conf{crossing_link}{index}{$pair}{cross_link_anchor_pos}:$conf{cross_link_anchor_pos};
my $left_up_x = $conf{crossing_link}{position}{$up_id}{start}{x};
my $left_up_y = $conf{crossing_link}{position}{$up_id}{start}{y};
my $right_up_x = $conf{crossing_link}{position}{$up_id}{end}{x};
my $right_up_y = $conf{crossing_link}{position}{$up_id}{end}{y};
if($cross_link_anchor_pos=~ /^up_/){
$left_up_y-=$conf{feature_setting}{$up_id}{cross_link_shift_y};
$right_up_y-=$conf{feature_setting}{$up_id}{cross_link_shift_y};
}elsif($cross_link_anchor_pos=~ /^low_/){
$left_up_y+=$conf{feature_setting}{$up_id}{cross_link_shift_y};
$right_up_y+=$conf{feature_setting}{$up_id}{cross_link_shift_y};
}elsif($cross_link_anchor_pos !~ /^medium_/){
die "error: not support $conf{cross_link_anchor_pos} yet~\n"
}
my $left_down_x = $conf{crossing_link}{position}{$down_id}{start}{x};
my $left_down_y = $conf{crossing_link}{position}{$down_id}{start}{y};
my $right_down_x = $conf{crossing_link}{position}{$down_id}{end}{x};
my $right_down_y = $conf{crossing_link}{position}{$down_id}{end}{y};
if($cross_link_anchor_pos=~ /_low$/){
$left_down_y+=$conf{feature_setting}{$down_id}{cross_link_shift_y};
$right_down_y+=$conf{feature_setting}{$down_id}{cross_link_shift_y};
}elsif($cross_link_anchor_pos=~ /_up$/){
$left_down_y-=$conf{feature_setting}{$down_id}{cross_link_shift_y};
$right_down_y-=$conf{feature_setting}{$down_id}{cross_link_shift_y};
}elsif($cross_link_anchor_pos !~ /_medium$/){
die "error: not support $conf{cross_link_anchor_pos} yet~\n"
}
$orders{$cross_link_order}.="<polygon points=\"$left_up_x,$left_up_y $right_up_x,$right_up_y $right_down_x,$right_down_y $left_down_x,$left_down_y\" style=\"fill:$color;stroke:#000000;stroke-width:0;opacity:$cross_link_opacity\"/>\n"; #crossing link of features
#print "link corlis $color\n";
}
## draw legend
my $legend_num=0;
my %legend_color_num;
for my $f(keys %{$conf{feature_setting}}){
if(exists $conf{feature_setting}{$f}{legend_label}){
if(exists $legend_color_num{$conf{feature_setting}{$f}{feature_color}}){
if($legend_color_num{$conf{feature_setting}{$f}{feature_color}} ne $conf{feature_setting}{$f}{legend_label}){
die "error: one $conf{feature_setting}{$f}{feature_color} -> more than one different legend_label\n";
}
}else{
$legend_color_num{$conf{feature_setting}{$f}{feature_color}}=$conf{feature_setting}{$f}{legend_label};
}
}
}
$legend_num=keys %legend_color_num;
#print "legend_num is $legend_num\n";
#my $top_margin_legend;
#my $legend_single_arrow_height = $common_size; # 和sample name一样的字体大小，字体大小几乎等同同等像素的宽高
#my $limit = 0.8;
#if($legend_single_arrow_height*$legend_num < $svg_height*$limit){
# $top_margin_legend = $svg_height - $legend_single_arrow_height*$legend_num *1.1; #第一个legend顶部的y轴
#}else{
# $legend_single_arrow_height = $svg_height*$limit/$legend_num;# 每行legend的高度
# $top_margin_legend = (1-$limit)/2*$svg_height;
#}
#my $legend_font_size = $legend_single_arrow_height * 0.9;
#my $legend_max_length=0;
#foreach my $legend(keys %{$conf{feature_setting}{legend_col}}){
# if(length($legend) >$legend_max_length){
# $legend_max_length = $length($legend);
# }
#}
if($conf{display_legend}=~ /yes/i){
print "lengend start\n";
my $legend_arrow_height = $id_line_height*$conf{feature_height_ratio}*$conf{legend_height_ratio};
my $legend_font_size = $conf{legend_font_size}; #legend中文字字体大小
my $top_margin_legend = ($svg_height - ($legend_arrow_height * $legend_num + ($legend_num-1)*$legend_arrow_height*$conf{legend_height_space}))/2;
my $legend_single_arrow_height = $legend_arrow_height;
my $legend_width_margin = $conf{legend_width_margin};
my $legend_width_textpercent = $conf{legend_width_textpercent};
my $legend_arrow_width = (1-$legend_width_margin*2)*(1-$legend_width_textpercent)*$svg_width*$legend_width_ratio;
my $text_x = (1-$legend_width_ratio)*$svg_width+$legend_width_margin*$legend_width_ratio*$svg_width+$legend_arrow_width*1.2;
my $text_y = $top_margin_legend + 0.95*$legend_arrow_height ;
my $arrow_x = (1-$legend_width_ratio)*$svg_width+$legend_width_margin*$legend_width_ratio*$svg_width*1.1;
my $arrow_y = $top_margin_legend;
#my $legend_arrow_height = $legend_single_arrow_height * 0.8;
foreach my $legend_color(sort keys %legend_color_num){
my $legend = $legend_color_num{$legend_color};
## draw_gene 函数需要重写，输入起点的xy坐标，正负链等信息即可
# 先用方块代替arrow
my @arr_cols=split(/,,/, $legend_color);
my $arrow_col_start;
my $arrow_col_end;
#print "legend arr_cols is @arr_cols\n";
if(@arr_cols==2){
#print "aisis $conf{feature_setting}{legend_col}{$legend},@arr_cols\n";
$arrow_col_start = $arr_cols[0];
$arrow_col_end = $arr_cols[1];
#my $arrow_color_id = $conf{feature_setting}{legend_col}{$legend};
my $arrow_color_id = $legend_color;
$arrow_color_id=~ s/,/-/g;
$arrow_color_id=~ s/\)/-/g;
$arrow_color_id=~ s/\(/-/g;
$svg.="
<defs>
<linearGradient id=\"$arrow_color_id\" x1=\"0%\" y1=\"0%\" x2=\"0%\" y2=\"100%\">
<stop offset=\"0%\" style=\"stop-color:$arrow_col_start;stop-opacity:1\"/>
<stop offset=\"50%\" style=\"stop-color:$arrow_col_end;stop-opacity:1\"/>
<stop offset=\"100%\" style=\"stop-color:$arrow_col_start;stop-opacity:1\"/>
</linearGradient>
</defs>
<g style=\"fill:none\">
<rect x=\"$arrow_x\" y=\"$arrow_y\" width=\"$legend_arrow_width\" height=\"$legend_arrow_height\" style=\"fill:url(#$arrow_color_id);stroke:black;stroke-width:1;fill-opacity:1;stroke-opacity:1\" />
</g>";
}else{
$svg.="<rect x=\"$arrow_x\" y=\"$arrow_y\" width=\"$legend_arrow_width\" height=\"$legend_arrow_height\" style=\"fill:$legend_color;stroke:$conf{legend_stroke_color};stroke-width:$conf{legend_stroke_width};fill-opacity:1;stroke-opacity:1\" />";
}
## draw legend
$svg.="<text x=\"$text_x\" y=\"$text_y\" font-size=\"${legend_font_size}px\" fill=\"black\" text-anchor='start'>$legend</text>";
$arrow_y += $legend_single_arrow_height +$legend_arrow_height*$conf{legend_height_space};
$text_y += $legend_single_arrow_height +$legend_arrow_height*$conf{legend_height_space};
## draw legend
}
#legend外围的线框
#my $legend_rect_width = (1-$legend_width_margin*2)*$svg_width*$legend_width_ratio * 1.1;
#my $legend_rect_height = $svg_height*$legend_height_percent * 1.04;
#my $legend_rect_x = (1-$legend_width_ratio)*$svg_width+$legend_width_margin*$legend_width_ratio*$svg_width *0.9;
#my $legend_rect_y = $top_margin_legend;
#$svg.="<rect x=\"$legend_rect_x\" y=\"$legend_rect_y\" width=\"$legend_rect_width\" height=\"$legend_rect_height\" style=\"fill:none;stroke:black;stroke-width:1;fill-opacity:0;stroke-opacity:1\" />"; #不画这条线框了
}
#刻度尺
if($conf{scale_display}=~ /yes/i){
my @scales=split(/_/, $conf{scale_position});
foreach my $scale(@scales){
print "disply scale\n";
my $x_start_scale=$left_distance_init;
#my $x_end_scale=$cluster_width_ratio*$svg_width + $x_start_scale - $space_len;
my $x_end_scale=$cluster_width_ratio*$svg_width + $x_start_scale;
my $y_scale;
my $y_tick_shift=-3;
my $font_size=$conf{scale_tick_fontsize};
my $tick_height=$conf{scale_tick_height}* $svg_height;
if($scale=~ /up/){
$y_scale=$top_bottom_margin/2* 0.5 * (1-$conf{scale_padding_y})* $svg_height;
#$y_tick_shift=-$conf{scale_tick_padding_y};
}else{
$y_scale=(1- $top_bottom_margin/2*(1-$conf{scale_padding_y})) * $svg_height;
$y_tick_shift=$conf{scale_tick_padding_y};
$tick_height=-$tick_height;
}
$orders{$conf{scale_order}}.="<line x1=\"$x_start_scale\" y1=\"$y_scale\" x2=\"$x_end_scale\" y2=\"$y_scale\" style=\"stroke:$conf{scale_color};stroke-width:$conf{scale_width}\"/>\n"; #main line
my $unit_scale=$conf{scale_ratio}*$ratio; # bp
my $ticks=int($cluster_width_ratio*$svg_width/$unit_scale);
print "ticks number is $ticks\n";
my $tick_y1= $y_scale + $tick_height; #single tick hegith
my $tick_y2= $y_scale ;
my $tick_label_y=$y_scale+$y_tick_shift;
foreach my $tick(0..$ticks){
my $tick_x=$tick*$unit_scale + $x_start_scale;
my $tick_label=$tick*$conf{scale_ratio};
$orders{$conf{scale_order}}.="<line x1=\"$tick_x\" y1=\"$tick_y1\" x2=\"$tick_x\" y2=\"$tick_y2\" style=\"stroke:$conf{scale_color};stroke-width:$conf{scale_width};opacity:$conf{scale_tick_opacity}\"/>\n"; # ticks
$orders{$conf{scale_order}}.= "<text x=\"$tick_x\" y=\"$tick_label_y\" font-size=\"${font_size}px\" fill=\"$conf{scale_color}\" text-anchor='middle' font-family=\"Times New Roman\">$tick_label</text>\n"; # label of feature
}
if($cluster_width_ratio*$svg_width % $unit_scale){
$orders{$conf{scale_order}}.="<line x1=\"$x_end_scale\" y1=\"$tick_y1\" x2=\"$x_end_scale\" y2=\"$tick_y2\" style=\"stroke:$conf{scale_color};stroke-width:$conf{scale_width};opacity:$conf{scale_tick_opacity}\"/>\n"; # last tick
my $last_tick_label=$max_length;
$orders{$conf{scale_order}}.= "<text x=\"$x_end_scale\" y=\"$tick_label_y\" font-size=\"${font_size}px\" fill=\"$conf{scale_color}\" text-anchor='middle' font-family=\"Times New Roman\">$last_tick_label</text>\n"; # label of feature
}
}
}
open SVG,">$outdir/$prefix.svg" or die "$!";
print SVG "$svg";
for my $order(sort {$a<=>$b}keys %orders){
print "order is $order\n";
print SVG "\n$orders{$order}\n";
}
print SVG "</svg>";
close SVG;
print "outfile is $outdir/$prefix.svg\n";
`set -vex;convert $outdir/$prefix.svg $outdir/$prefix.png ; echo outfile is $outdir/$prefix.png; convert -density $conf{pdf_dpi} $outdir/$prefix.svg $outdir/$prefix.dpi$conf{pdf_dpi}.pdf;echo outfile is $outdir/$prefix.dpi$conf{pdf_dpi}.pdf`;
#$svg.=&draw_genes($gff{$sample}{id}{$id}{$index}{start},$gff{$sample}{id}{$id}{$index}{end},$gff{$sample}{id}{$id}{$index}{strand},$gene_height_medium,$gene_height_top);
sub read_list(){
###start:get scaffold length in genome file and scaffold length in gff file
my ($list) = @_;
my (%genome,%gff,$sample_num);
my @features=split(/,/, $conf{feature_keywords});
my %uniq_sample;
open LI,"$list" or die "$!";
while(<LI>){
chomp;
next if($_=~ /^\s*$/||$_=~ /^#/);
$sample_num++;
my $block_index=1;
my %scf_block_id;
my ($sample,$gffs,$genome,@arrs)=split(/\t/,$_); # $seq_id,$seq_draw_start,$seq_draw_end
if(exists $uniq_sample{$sample}){
die "error:more than one $sample, not allow same 1th column in $list~\n "
}else{
$uniq_sample{$sample}="";
}
print "$sample\n";
if(@arrs%3){
die "$list line $. error format:$_, should be separated by \\t \n";
}
open GE,"$genome" or die "$!";
$/=">";<GE>;
while(<GE>){
chomp;
my ($id,$seq)=split(/\n/,$_,2);
$id=~ /^(\S+)/;
$id=$1;
$seq=~ s/\s+//g;
my $len=length $seq;
$genome{$sample}{$id}{len}=$len;
}
close GE;
$/="\n";
my %all_seq_id;
open GFF,"$gffs" or die "$!";
while(<GFF>){
chomp;
next if($_=~ /^#/);
my @arr=split(/\t/,$_);
$all_seq_id{$arr[0]} = "";
}
close GFF;
open GFF,"$gffs" or die "$!";
my $gene_index;
while(<GFF>){
chomp;
next if($_=~ /^#/);
my @arr=split(/\t/,$_);
die "error: $gffs should have tab in file~\n" if(@arr==1);
my $block_index=-1;
my $start_f=$arr[3];
my $end_f=$arr[4];
if($arr[3] > $arr[4]){
$arr[3] = $end_f;
$arr[4] = $start_f;
}
if(@arrs){ # has seq_id mean not full length of whole gff
#my $xxx=scalar(@arrs);
#if ($xxx == 9){
# print "arrs is $xxx,$sample @arrs end\n";
#}
for (my $arrs_index=0;$arrs_index < scalar(@arrs);$arrs_index+=3){
my ($seq_id,$seq_draw_start,$seq_draw_end) = @arrs[$arrs_index..$arrs_index+2];
die "error: $seq_id not in $gffs\n" if(not exists $all_seq_id{$seq_id});
my $seq_draw_start_tmp=$seq_draw_start;
my $seq_draw_end_tmp=$seq_draw_end;
$seq_draw_start = eval($seq_draw_start);
$seq_draw_end = eval($seq_draw_end);
die "error:for $seq_id , start $seq_draw_start_tmp should less than end $seq_draw_end_tmp in --list " if($seq_draw_end <= $seq_draw_start);
#print "$seq_id,$seq_draw_start,$seq_draw_end\n";
next unless ($arr[0] eq $seq_id && $arr[3] >= $seq_draw_start && $arr[4] <= $seq_draw_end);
$seq_draw_end = ($genome{$sample}{$seq_id}{len}>=$seq_draw_end)? $seq_draw_end:$genome{$sample}{$seq_id}{len}; #防止seq_draw_end越界
$genome{$sample}{$arr[0]}{$arrs_index}{len}=$seq_draw_end -$seq_draw_start+1; # 一条scaffold有多个block
$arr[3]=$arr[3]-$seq_draw_start +1;
$arr[4]=$arr[4]-$seq_draw_start +1;
$block_index = $arrs_index;
#print "hereis $block_index\n";
if(not exists $gff{$sample}{chooselen_single}{$block_index}){
$gff{$sample}{chooselen_single}{$block_index}{len} = $genome{$sample}{$arr[0]}{$arrs_index}{len};
$gff{$sample}{chooselen_single}{$block_index}{start} = $seq_draw_start;
$gff{$sample}{chooselen_single}{$block_index}{end} = $seq_draw_end;
#gff{$sample}{chooselen_single}{$block_index}{scf_id} = $arr[0];
$gff{$sample}{chooselen_all} +=$gff{$sample}{chooselen_single}{$block_index}{len}; ## 把每行所有block长度加起来
$gff{$sample}{chooselen_all} += $space_len ; ## 加上 每个block之间的宽度，500bp相当于一个基因的长度,后面最好把这个500bp改成每个track实际的平均基因长度
}
}
}else{ # list里面没有定义seq_id/start/end,即要画full-length of scaffold
#print "not seq_id\n";
#$block_index = $conf{'scaffold_order'}{$sample}{$arr[0]};
$scf_block_id{$arr[0]} = $. if(not exists $scf_block_id{$arr[0]});
$block_index=$scf_block_id{$arr[0]};
if(not exists $gff{$sample}{chooselen_single}{$block_index}){
$gff{$sample}{chooselen_single}{$block_index}{len} = $genome{$sample}{$arr[0]}{len};
$gff{$sample}{chooselen_single}{$block_index}{start} = 1;
$gff{$sample}{chooselen_single}{$block_index}{end} = $genome{$sample}{$arr[0]}{len};
$gff{$sample}{chooselen_all} +=$gff{$sample}{chooselen_single}{$block_index}{len}; # ## 把每行所有block(即scaffold)长度加起来
#print "$sample $gff{$sample}{chooselen_all}\n";
$gff{$sample}{chooselen_all} += $space_len ; ## 这个500最好改成每个track的blocks的平均长度的一定比例，比如一半
}
#$gff{$sample}{block}{$block_index}{$arr[0]}{len}=$genome{$sample}{$arr[0]}{len}; # 一条scaffold就是一个block
}
#print "block $sample $block_index\n";
#next if($arr[2] ne "gene" || $block_index == -1); ## 目前的只是画基因的cluster,后面会把其他组分也加进去
next if(@arrs && $block_index == -1);
my $flag=1;
foreach my $f(@features){
next if ($f=~ /^\s*$/);
$f=~ s/\s//g;
$flag =0 if($arr[2]=~ /$f/);
}
next if($flag);
$_=~ /\sID=([^;]+);/;
my $feature_id=$1;
die "error: $feature_id in $gffs should not contain , \n" if($feature_id=~ /,/);
$gene_index++;
if(!$arr[3]){die "error:$gffs line $.\n"}
$gff{$sample}{block}{$block_index}{$arr[0]}{$gene_index}{start}=$arr[3]; # block_index 是指每行中每个cluster的左右顺序
$gff{$sample}{block}{$block_index}{$arr[0]}{$gene_index}{start_raw}=$start_f; # block_index 是指每行中每个cluster的左右顺序
$gff{$sample}{block}{$block_index}{$arr[0]}{$gene_index}{end}=$arr[4];
$gff{$sample}{block}{$block_index}{$arr[0]}{$gene_index}{end_raw}=$end_f;
$gff{$sample}{block}{$block_index}{$arr[0]}{$gene_index}{id}=$feature_id;
if(!$feature_id){die "die:line is $_\n"}
$gff{$sample}{block}{$block_index}{$arr[0]}{$gene_index}{strand}=($arr[6]=~ /\+/)? 1:0;
#foreach my $index(sort {$gff{$sample}{block}{$block_index}{$scf[0]}{$a}{start}<=>$gff{$sample}{block}{$block_index}{$scf[0]}{$b}{start}} keys %{$gff{$sample}{block}{$block_index}{$scf[0]}}){
$conf{feature_setting}{$feature_id}{start}=$start_f;
$conf{feature_setting}{$feature_id}{end}=$end_f;
$conf{feature_setting}{$feature_id}{sample}=$sample;
$conf{feature_setting}{$feature_id}{scf_id}=$arr[0];
#print "block $sample $block_index $arr[0] $gene_index $arr[3] $arr[4] $feature_id\n";
#print "id is $feature_id\n";
}
close GFF;
}
close LI;
return (\%genome, \%gff, $sample_num);
####end:get scaffold length in genome file and scaffold length in gff file
}
sub draw_genes(){
#draw_genes($index_id, $index_start, $index_end, $index_strand, $gene_height_medium, $gene_height_top, $gene_width_arrow, $shift_x, $top_distance, $sample_single_height, $sample, $scf[0], $index_color, $index_label_content, $index_label_size, $index_label_col, $index_label_position, $index_label_angle, $angle_flag); ## draw_gene 函数需要重写，输入起点的xy坐标，正负链等信息即可
my ($feature_id,$start,$end,$strand,$start_raw,$end_raw,$gene_height_medium,$gene_height_top,$gene_width_arrow,$shift_x,$shift_y,$feature_shift_y,$sample_single_height,$sample,$id, $index_color, $index_label_content, $index_label_size, $index_label_col, $index_label_position, $index_label_angle, $angle_flag)=@_;
if($index_color=~ /rgb\(\d+,\d+,\d+\),[^,]/ or $index_color=~ /[^,],rgb\(\d+,\d+,\d+\)/){
die "\nerror: should use ,, instead of , to separate the $index_color\n";
}
my @arr_cols = split(/,,/, $index_color);
for my $c (@arr_cols){
if($c!~ /^rgb/ && $c!~ /^#\d+$/ && $c!~ /^\w/){
die "error: $c for @arr_cols of $feature_id is wrong color format\n";
}
}
my $feature_opacity=(exists $conf{feature_setting}{$feature_id}{feature_opacity})? $conf{feature_setting}{$feature_id}{feature_opacity}:$conf{feature_opacity};
my $shape=$conf{feature_shape};
$shape=(exists $conf{feature_setting}{$feature_id}{feature_shape})? $conf{feature_setting}{$feature_id}{feature_shape}:$conf{feature_shape};
my $shift_unit=$id_line_height;
if($shape=~ /^circle_point/){
$shift_unit=($end-$start)*$ratio;
}
if($feature_shift_y=~ /^\s*([+-])([\d\.]+)/){
if($1 eq "+"){
$shift_y += -1 * $2 * $shift_unit - 0.5 * $id_line_height;
}else{
$shift_y += 1 * $2 * $shift_unit + 0.5 * $id_line_height;
}
}elsif($feature_shift_y=~ /^\s*0/){
$shift_y +=0
}else{
die "error: for $feature_id, feature_shift_y should be like +1 or -1, +2, so on\n"
}
my $order_f=(exists $conf{feature_setting}{$feature_id}{feature_order})? $conf{feature_setting}{$feature_id}{feature_order}:$conf{feature_order};
my $order_f_label=(exists $conf{feature_setting}{$feature_id}{feature_label_order})? $conf{feature_setting}{$feature_id}{feature_label_order}:$conf{feature_label_order};
my $padding_feature_label=(exists $conf{feature_setting}{$feature_id}{padding_feature_label})? $conf{feature_setting}{$feature_id}{padding_feature_label}:$conf{padding_feature_label};
my $display_feature=(exists $conf{feature_setting}{$feature_id}{display_feature})? $conf{feature_setting}{$feature_setting}{display_feature}:$conf{display_feature};
my $display_feature_label=(exists $conf{feature_setting}{$feature_id}{display_feature_label})? $conf{feature_setting}{$feature_setting}{display_feature_label}:$conf{display_feature_label};
#<circle cx=\"$center_point_x\" cy=\"$center_point_y\" r=\"$radius\" stroke=\"$feature_stroke_color\" stroke-width=\"$feature_stroke_size\" fill=\"$feature_color\"/>
my $feature_stroke_color=(exists $conf{feature_setting}{$feature_id}{feature_border_color})? $conf{feature_setting}{$feature_id}{feature_border_color}:$conf{feature_border_color};
my $feature_stroke_size= (exists $conf{feature_setting}{$feature_id}{feature_border_size})? $conf{feature_setting}{$feature_id}{feature_border_size}:$conf{feature_border_size};
my ($back,$x1,$y1,$x2,$y2,$x3,$y3,$x4,$y4,$x5,$y5,$x6,$y6,$x7,$y7,$label_x,$label_y,$index_col_start,$index_col_end,$crossing_link_start_x,$crossing_link_start_y,$crossing_link_end_x,$crossing_link_end_y);
my ($label_y_shift, $label_roat_angle);
$back="";
#print "distance_closed_feature $conf{distance_closed_feature}\n";
if($angle_flag){
$shift_angle_closed_feature += $conf{shift_angle_closed_feature};
}else{
$shift_angle_closed_feature = 0;
}
if($index_label_position=~ /_up$/){
$label_y_shift= - $padding_feature_label;
$index_label_angle = ($angle_flag)? $index_label_angle +$shift_angle_closed_feature:$index_label_angle; # 相邻feature的label的angle开
}elsif($index_label_position=~ /_low$/){
$label_y_shift= 2*$gene_height_top+$gene_height_medium + $padding_feature_label;
$index_label_angle = ($angle_flag)? $index_label_angle -$shift_angle_closed_feature:$index_label_angle; # 相邻feature的label的angle开
}elsif($index_label_position=~ /_medium$/){
$label_y_shift= $gene_height_top+0.5*$gene_height_medium + $padding_feature_label;
$index_label_angle = ($angle_flag)? $index_label_angle -$shift_angle_closed_feature:$index_label_angle; # 相邻feature的label的angle开
}else{
die "error: not support $conf{pos_feature_label} yet~\n"
}
my $start_title=$start;
my $end_title=$end;
if($conf{absolute_postion_in_title}=~ /yes/i){
$start_title=$start_raw;
$end_title=$end_raw;
}
if($shape=~ /arrow/){
if($strand){
#以左上角为起始点，逆时针转一圈
$x1=($start*$ratio+$shift_x);$y1=($sample_single_height - $gene_height_medium)/2+$shift_y;#gene_height_medium指arrow中间的高度
$x2=$x1;$y2=$y1+$gene_height_medium;
$x3=$x2+(1-$gene_width_arrow)*($end -$start)*$ratio;$y3=$y2;#gene_width_arrow指横向的arrow箭头的宽度
$x4=$x3;$y4=$y3+$gene_height_top; ##gene_height_top是指arrow中间之外的一边尖尖的高度
$x5=$x2+($end -$start)*$ratio;$y5=0.5*$sample_single_height+$shift_y;
$x6=$x4;$y6=$y4 - 2*$gene_height_top - $gene_height_medium;
$x7=$x3;$y7=$y1;
$label_y=$y6+$label_y_shift;
$crossing_link_start_x=$x1;
$crossing_link_start_y=$y1+0.5*$gene_height_medium;
$crossing_link_end_x=$x5;
$crossing_link_end_y=$y5;
}else{
#负链以arrow左边尖尖为起始点，逆时针旋转一周
$x1=($start*$ratio+$shift_x);$y1=0.5*$sample_single_height+$shift_y;
$x2=$x1+$gene_width_arrow*($end -$start)*$ratio;$y2=$y1+0.5*$gene_height_medium+$gene_height_top;
$x3=$x2;$y3=$y2 -$gene_height_top;
$x4=$x3+(1-$gene_width_arrow)*($end -$start)*$ratio;$y4=$y3;
$x5=$x4;$y5=$y4-$gene_height_medium;
$x6=$x3;$y6=$y5;
$x7=$x2;$y7=$y2 -2*$gene_height_top - $gene_height_medium;
$label_y=$y7+$label_y_shift;
$crossing_link_start_x=$x1;
$crossing_link_start_y=$y1;
$crossing_link_end_x=$x4;
$crossing_link_end_y=$y4-0.5*$gene_height_medium;
}
if($index_label_position=~ /^medium_/){
$label_x = $x1 + ($end - $start)/2 * $ratio;
}elsif($index_label_position=~ /^left_/){
$label_x = $x1;
}elsif($index_label_position=~ /^right_/){
$label_x = $x4;
}else{
die "error: not support $conf{pos_feature_label} yet~\n"
}
#print "index_color2 is $index_color\n";
if(@arr_cols==2 && $display_feature=~ /yes/i){
$index_col_start = $arr_cols[0];
$index_col_end = $arr_cols[1];
my $index_color_id = $index_color;
$index_color_id=~ s/,/-/g;
$index_color_id=~ s/\)/-/g;
$index_color_id=~ s/\(/-/g;
$orders{$order_f}.="
<defs>
<linearGradient id=\"$index_color_id\" x1=\"0%\" y1=\"0%\" x2=\"0%\" y2=\"100%\">
<stop offset=\"0%\" style=\"stop-color:$index_col_start;stop-opacity:1\"/>
<stop offset=\"50%\" style=\"stop-color:$index_col_end;stop-opacity:1\"/>
<stop offset=\"100%\" style=\"stop-color:$index_col_start;stop-opacity:1\"/>
</linearGradient>
</defs>
<g style=\"fill:none\">
<title>$feature_id,$sample,$id,$start_title,$end_title,$strand</title>
<polygon points=\"$x1,$y1 $x2,$y2 $x3,$y3 $x4,$y4 $x5,$y5 $x6,$y6 $x7,$y7\" style=\"fill:url(#$index_color_id);stroke:$feature_stroke_color;stroke-width:$feature_stroke_size;opacity:$feature_opacity\"/>
</g>\n"; ## feture arrow
}elsif($display_feature=~ /yes/i){
$orders{$order_f}.="
<g style=\"fill:none\">
<title>$feature_id,$sample,$id,$start_title,$end_title,$strand</title>
<polygon points=\"$x1,$y1 $x2,$y2 $x3,$y3 $x4,$y4 $x5,$y5 $x6,$y6 $x7,$y7\" style=\"fill:$index_color;stroke:$feature_stroke_color;stroke-width:$feature_stroke_size;opacity:$feature_opacity\"/>
</g>\n"; ## feture arrow
}
## draw label of feature
$orders{$order_f_label}.= "<text x=\"$label_x\" y=\"$label_y\" font-size=\"${index_label_size}px\" fill=\"$index_label_col\" text-anchor='start' transform=\"rotate($index_label_angle $label_x $label_y)\" font-family=\"Times New Roman\">$index_label_content</text>\n" if($display_feature_label!~ /no/i && $display_feature_label!~ /no,no/i ); # label of feature
#$svg.="<text x=\"$ref_name_x\" y=\"$ref_name_y\" font-size=\"${text_size}px\" fill=\"$conf{color_sample_name}\" text-anchor='end'>$conf{sample_name_old2new}{$sample}</text>\n";
# check this feature if is in crossing_link
if(exists $conf{crossing_link}{features}{$feature_id}){
#print "crossing_link $feature_id\n";
$conf{crossing_link}{position}{$feature_id}{start}{x}=$crossing_link_start_x;
$conf{crossing_link}{position}{$feature_id}{start}{y}=$crossing_link_start_y;
$conf{crossing_link}{position}{$feature_id}{end}{x}=$crossing_link_end_x;
$conf{crossing_link}{position}{$feature_id}{end}{y}=$crossing_link_end_y;
#print "crossing_linkis $feature_id $crossing_link_start_x $crossing_link_start_y $crossing_link_end_x $crossing_link_end_y\n";
}
}elsif($shape=~ /^rect/){
if($strand){
#以左上角为起始点，逆时针转一圈
$x1=($start*$ratio+$shift_x);$y1=($sample_single_height - $gene_height_medium)/2+$shift_y;#gene_height_medium指arrow中间的高度
$x2=$x1;$y2=$y1+$gene_height_medium;
$x3=$x2+($end -$start)*$ratio;$y3=$y2;
$x4=$x3;$y4=$y1;
$label_y=$y4+$label_y_shift;
$crossing_link_start_x=$x1;
$crossing_link_start_y=$y1+0.5*$gene_height_medium;
$crossing_link_end_x=$x3;
$crossing_link_end_y=$crossing_link_start_y;
}else{
#以左上角为起始点，逆时针转一圈
$x1=($start*$ratio+$shift_x);$y1=($sample_single_height - $gene_height_medium)/2+$shift_y;#gene_height_medium指arrow中间的高度
$x2=$x1;$y2=$y1+$gene_height_medium;
$x3=$x2+($end -$start)*$ratio;$y3=$y2;
$x4=$x3;$y4=$y1;
$label_y=$y4+$label_y_shift;
$crossing_link_start_x=$x1;
$crossing_link_start_y=$y1+0.5*$gene_height_medium;
$crossing_link_end_x=$x3;
$crossing_link_end_y=$crossing_link_start_y;
}
if($index_label_position=~ /^medium_/){
$label_x = $x1 + ($end - $start)/2 * $ratio;
}elsif($index_label_position=~ /^left_/){
$label_x = $x1;
}elsif($index_label_position=~ /^right_/){
$label_x = $x4;
}else{
die "error: not support $conf{pos_feature_label} yet~\n"
}
#print "y1 is $y1\n";
#my ($feature_id,$start,$end,$strand,$gene_height_medium,$gene_height_top,$gene_width_arrow,$shift_x,$shift_y,$sample_single_height,$sample,$id, $index_color, $index_label, $index_label_content, $index_label_size, $index_label_col, $index_label_position, $index_label_angle)=@_;
#print "index_color2 is $index_color\n";
if(@arr_cols==2 && $display_feature=~ /yes/i){
$index_col_start = $arr_cols[0];
$index_col_end = $arr_cols[1];
my $index_color_id = $index_color;
$index_color_id=~ s/,/-/g;
$index_color_id=~ s/\)/-/g;
$index_color_id=~ s/\(/-/g;
$orders{$order_f}.="
<defs>
<linearGradient id=\"$index_color_id\" x1=\"0%\" y1=\"0%\" x2=\"0%\" y2=\"100%\">
<stop offset=\"0%\" style=\"stop-color:$index_col_start;stop-opacity:1\"/>
<stop offset=\"50%\" style=\"stop-color:$index_col_end;stop-opacity:1\"/>
<stop offset=\"100%\" style=\"stop-color:$index_col_start;stop-opacity:1\"/>
</linearGradient>
</defs>
<g style=\"fill:none\">
<title>$feature_id,$sample,$id,$start_title,$end_title,$strand</title>
<polygon points=\"$x1,$y1 $x2,$y2 $x3,$y3 $x4,$y4 \" style=\"fill:url(#$index_color_id);stroke:$feature_stroke_color;stroke-width:$feature_stroke_size;opacity:$feature_opacity\"/>
</g>\n"; ## feture rect
}elsif($display_feature=~ /yes/i){
$orders{$order_f}.="
<g style=\"fill:none\">
<title>$feature_id,$sample,$id,$start_title,$end_title,$strand</title>
<polygon points=\"$x1,$y1 $x2,$y2 $x3,$y3 $x4,$y4 \" style=\"fill:$index_color;stroke:$feature_stroke_color;stroke-width:$feature_stroke_size;opacity:$feature_opacity\"/>
</g>\n"; ## feture rect
}
## draw label of feature
$orders{$order_f_label}.= "<text x=\"$label_x\" y=\"$label_y\" font-size=\"${index_label_size}px\" fill=\"$index_label_col\" text-anchor='start' transform=\"rotate($index_label_angle $label_x $label_y)\" font-family=\"Times New Roman\">$index_label_content</text>\n" if($display_feature_label!~ /no/i && $display_feature_label!~ /no,no/i); # label of feature
# check this feature if is in crossing_link
if(exists $conf{crossing_link}{features}{$feature_id}){
#print "crossing_link $feature_id\n";
$conf{crossing_link}{position}{$feature_id}{start}{x}=$crossing_link_start_x;
$conf{crossing_link}{position}{$feature_id}{start}{y}=$crossing_link_start_y;
$conf{crossing_link}{position}{$feature_id}{end}{x}=$crossing_link_end_x;
$conf{crossing_link}{position}{$feature_id}{end}{y}=$crossing_link_end_y;
#print "crossing_linkis $feature_id $crossing_link_start_x $crossing_link_start_y $crossing_link_end_x $crossing_link_end_y\n";
}
}elsif($shape=~ /^round_rect/){
die "error: not support $shape yet~\n";
}elsif($shape=~ /^circle_point/){
my $center_point_x=$start*$ratio + $shift_x + ($end - $start)*$ratio*0.5;
my $center_point_y=($sample_single_height - $gene_height_medium)/2 + $shift_y + 0.5*$gene_height_medium ;
my $radius= ($end - $start)*$ratio*0.5 ; # 0.5*$gene_height_medium;
my $x1=$start*$ratio+$shift_x;
my $x4=$x1+($end-$start)*$ratio;
my $crossing_link_start_x=$center_point_x;
my $crossing_link_start_y=$center_point_y-$radius;
my $crossing_link_end_x=$center_point_x;
my $crossing_link_end_y=$center_point_y+$radius;
if($index_label_position=~ /^medium_/){
$label_x = $x1 + ($end - $start)/2 * $ratio;
}elsif($index_label_position=~ /^left_/){
$label_x = $x1;
}elsif($index_label_position=~ /^right_/){
$label_x = $x4;
}else{
die "error: not support $conf{pos_feature_label} yet~\n"
}
if(@arr_cols==2 && $display_feature=~ /yes/i){
$index_col_start = $arr_cols[0];
$index_col_end = $arr_cols[1];
my $index_color_id = $index_color;
$index_color_id=~ s/,/-/g;
$index_color_id=~ s/\)/-/g;
$index_color_id=~ s/\(/-/g;
$orders{$order_f}.="
<defs>
<linearGradient id=\"$index_color_id\" x1=\"0%\" y1=\"0%\" x2=\"0%\" y2=\"100%\">
<stop offset=\"0%\" style=\"stop-color:$index_col_start;stop-opacity:1\"/>
<stop offset=\"50%\" style=\"stop-color:$index_col_end;stop-opacity:1\"/>
<stop offset=\"100%\" style=\"stop-color:$index_col_start;stop-opacity:1\"/>
</linearGradient>
</defs>
<g style=\"fill:none\">
<title>$feature_id,$sample,$id,$start_title,$end_title,$strand</title>
<circle cx=\"$center_point_x\" cy=\"$center_point_y\" r=\"$radius\" stroke=\"$feature_stroke_color\" stroke-width=\"$feature_stroke_size\" fill=\"$index_color\" style=\"opacity:$feature_opacity\" />
</g>\n"; ## feture rect
}elsif($display_feature=~ /yes/i){
$orders{$order_f}.="
<g style=\"fill:none\">
<title>$feature_id,$sample,$id,$start_title,$end_title,$strand</title>
<circle cx=\"$center_point_x\" cy=\"$center_point_y\" r=\"$radius\" stroke=\"$feature_stroke_color\" stroke-width=\"$feature_stroke_size\" fill=\"$index_color\" style=\"opacity:$feature_opacity\"/>
</g>\n"; ## feture rect
}
## draw label of feature
$orders{$order_f_label}.= "<text x=\"$label_x\" y=\"$label_y\" font-size=\"${index_label_size}px\" fill=\"$index_label_col\" text-anchor='start' transform=\"rotate($index_label_angle $label_x $label_y)\" font-family=\"Times New Roman\">$index_label_content</text>\n" if($display_feature_label!~ /no/i && $display_feature_label!~ /no,no/i); # label of feature
# check this feature if is in crossing_link
if(exists $conf{crossing_link}{features}{$feature_id}){
#print "crossing_link $feature_id\n";
$conf{crossing_link}{position}{$feature_id}{start}{x}=$crossing_link_start_x;
$conf{crossing_link}{position}{$feature_id}{start}{y}=$crossing_link_start_y;
$conf{crossing_link}{position}{$feature_id}{end}{x}=$crossing_link_end_x;
$conf{crossing_link}{position}{$feature_id}{end}{y}=$crossing_link_end_y;
#print "crossing_linkis $feature_id $crossing_link_start_x $crossing_link_start_y $crossing_link_end_x $crossing_link_end_y\n";
}
#die "error: not support $shape yet~\n";
}else{
die "error: not support $shape yet~\n";
}
return $back;
}
sub display_conf(){
my (%conf) = @_;
foreach my $k (keys %conf){
if($k eq "sample_name_old2new"){
foreach my $old(keys %{$conf{$k}}){
print "$k\t$old\t$conf{$k}{$old}\n";
}
}elsif($k eq "feature_setting"){
foreach my $f(keys %{$conf{$k}}){
foreach my $e(keys %{$conf{$k}{$f}}){
print "$k\t$f\t$e\t$conf{$k}{$f}{$e}\n";
}
}
}elsif($k eq "crossing_link"){
foreach my $n(keys %{$conf{$k}}){
#print "$k\t$n\t@{$conf{$k}{$n}}\n";
print "$k\t$n\t\n";
}
}elsif($k eq "scaffold_order"){
for my $s(keys %{$conf{$k}}){
for my $index(keys %{$conf{$k}{$s}}){
print "$k\t$s\t$index\t$conf{$k}{$s}{$index}\n";
}
}
}else{
print "$k : $conf{$k}\n";
}
}
}
sub read_conf(){
my ($conf) = @_;
my %confs;
open IN, "$conf" or die "$!";
while(<IN>){
chomp;
next if($_=~ /^#/ || $_=~ /^\s*$/);
die "error: need = in $_ of $conf~\n" if($_!~ /=/);
$_=~ s/([^=^\s])\s+#.*$/$1/g;
my ($key, $value) = split(/\s*=\s*/, $_);
$value=~ s/\s+$//;
$value=~ s/^\s+//;
if(!$key){
print "line is $_\n";
}
$confs{$key} = $value;
print "$key -> $value\n";
}
close IN;
return %confs;
}
sub default_setting(){
my (%conf) = @_;
$conf{svg_width_height} ||= '600,1500';
#$conf{anchor_positon_ratio} ||= 1;
$conf{pdf_dpi} ||=100;
$conf{top_bottom_margin} ||=0.1;
$conf{genome_height_ratio} ||= 1;
$conf{feature_height_ratio} ||= 1.5;
$conf{space_between_blocks} ||= 1.1;
$conf{feature_label_size} ||=10;
$conf{feature_label_color} ||="black";
$conf{label_rotate_angle} ||=-60;
$conf{feature_color} ||= 'ForestGreen'; #ForestGreen,LimeGreen
$conf{color_sample_name_default} ||= 'green';
$conf{sample_name_color_default} ||='black';
$conf{sample_name_font_size_default} ||=15;
$conf{legend_font_size} ||= 15; #legend中文字字体大小
$conf{legend_height_percent} ||= 0.2; # legends的高度占整个图高度的比例
$conf{legend_width_margin} ||= 0.1; # legends左右两侧的margin
$conf{legend_width_textpercent} ||= 0.6; # l
$conf{feature_shape} ||= 'round_rect';
$conf{track_color} ||="green";
$conf{padding_feature_label} ||= 3;
$conf{pos_feature_label} ||="medium_up";
$conf{distance_closed_feature} ||=50;
$conf{shift_angle_closed_feature} ||=10;
$conf{feature_arrow_sharp_extent} =(defined $conf{feature_arrow_sharp_extent})? $conf{feature_arrow_sharp_extent}:0.3;
$conf{scale_display} ||="no";
$conf{scale_position} ||="low";
$conf{display_feature} ||="yes";
$conf{legend_stroke_color} ||="black";
$conf{legend_stroke_width} ||=0;
$conf{track_order}=(defined $conf{track_order})? $conf{track_order}:0;
$conf{feature_order} =(defined $conf{feature_order})? $conf{feature_order}:1;
$conf{feature_label_order} =(defined $conf{feature_label_order})? $conf{feature_label_order}:1;
$conf{cross_link_order} =(defined $conf{cross_link_order})? $conf{cross_link_order}:2; # bigger mean upper
$conf{cross_link_opacity} ||=1;
$conf{display_feature_label} ||="yes";
$conf{display_legend} ||="yes";
$conf{cross_link_anchor_pos} ||="medium_medium";
$conf{ignore_sharp_arrow} ||="no";
$conf{scale_color} ||="black";
$conf{scale_width} ||=1;
$conf{scale_ratio} ||=100;
$conf{scale_padding_y} ||=-0.1;
$conf{scale_tick_height} ||=0.01;
$conf{scale_tick_opacity} ||=0.5;
$conf{scale_order} ||=0;
$conf{scale_tick_padding_y} ||=10;
$conf{scale_tick_fontsize} ||=10;
$conf{feature_arrow_width_extent} ||=0.7;
$conf{connect_with_same_scaffold} ||="yes";
$conf{connect_stroke_dasharray} ||="2,2";
$conf{connect_stroke_width} ||=2;
$conf{connect_stroke_color} ||="black";
$conf{absolute_postion_in_title} ||="yes";