Too large svg graph to convert the format

[Yung-Chien]

Hi @hewm2008 , I'd drawm a svg graph with a range of 1.5 Mb contig and more than 10k bi-allelic snps. While the program report an error like this:

So how could I select the height value? Otherwise, a large chart convert program may need large memory , so how many memory should I to select in the perl script svg2xxx.pl? Thanks in anvances.

Best Regards, Yung-Chien

您好 @hewm2008 ， 我在做一个大约长1.5Mb的ld Block分析，其中包含了10k多的bi-allelic snps。这种分析首先产生了这样的一个错误：

我该如何选择Height参数呢？此外，由于svg转png这一步会消耗大量内存，设置一个低ppi的话会不会缩短运行时间以及节省内存呢？谢谢您。 祝好， Yung-Chien

[Yung-Chien]

Hi @hewm2008 , I found a other issue just before. When the range is too large, althouge I used "-InGFF" and "-NoGeneName" paramater, the output graph didn't display the annotation information, like this: What I expected is this: So how could I fix this problem? And what the colors(pink,blue and grey) means in the snp color bar? I guess the pink means a snp located in a coding region, but it confused me what the other color refered to.Thanks in advanced. Best Regards, Yung-Chien

[hewm2008]

For -InGFF : there are too many genes in the input region, the gene structure will not be displayed [-GeneLimtNum 30],you can set the parameter -GeneLimtNum larger，such as the [-GeneLimtNum 2000]; However, because the your input region is too large, gene structure may be drawn like a solid line

[hewm2008]

For Big SVG file ---- > png 1) convert command is recommended to be pre-installed, although it is not required. If your system does not have a convert command, svg2xxx.pl will be called. you can use the follow command to pre-install the convert command; sudo apt-get install ImageMagick or sudo yum install ImageMagick 2) You can manually turn the png canvas（低ppi） through the following command(通过修改画布大小即可以修改ppi):

   ` perl bin/svg_kit/svg2xxx.pl       xxxx.svg  -t   png    -height 50` 
    _perl bin/svg_kit/svg2xxx.pl  -h_   to see more parameters, including modifying ppi  (**-height 50**)
  also can be ( **-resize   4096**) : 
 ` convert  -resize   4096     xxxx.svg  xxxx.png`

 But it seems that the memory cannot be significantly reduced. Later, I have time to analyze and fix the initial canvas to reduce memory, instead of setting the canvas according to the snp size 。 后面有机会我将初始化画图的一开始的画布，从而减少内存，而不是由snp多少决定画布，这样才能减少内存 

3）Another way to reduce the memory: since the large number of sites call a large memory ,you can be randomly selected every xx bps.

[hewm2008]

@Yung-Chien 从截图上看并好像是 -h不能是小数，我再看了一下代码（ShowLDSVG：Line 1666行），是已经取整了，是不是你没有用最新版本？ 建议用最新的版本 or 你的手动运行一下 -height 50

perl bin/svg_kit/svg2xxx.pl xxxx.svg -t png -height 50

From your screenshot, it seems that -h cannot be a floating point number. I took a look at the latest code(ShowLDSVG:Line 1666) again and it has been rounded up. Did you not use the latest version?

It is recommended to use the latest version or run it manually -height 50

[Yung-Chien]

Hi @hewm2008 , Thanks for your reply, I solved the problem of -GeneLimtNum . And I found that the height issue seems not affect the program of plotting. Then I ignored it. But I still wonder what the color mean in the snp color bar(navy-blue,grey and pink) as below : Best Regards, Yung-Chien

[hewm2008]

@Yung-Chien 1 Use the latest version (>=1.37) will solve your problem ; also the following command : perl bin/svg_kit/svg2xxx.pl xxxx.svg -t png -height 50 perl bin/svg_kit/svg2xxx.pl -h to see more parameters, including modifying ppi (-height 50) also can be ( -resize 4096) : convert -resize 4096 xxxx.svg xxxx.png

2 the col mean can see from more help LDBlockShow-*/bin/ShowLDSVG -h

-crGene       <s>  : InColor for Gene Stuct [CDS:Intron:UTR:Intergenic] 
                                default ['#e7298a:lightblue:#7570b3:#a6cee3']

By the way to change the SpeSite col can be found -crTagSNP <s> : Color for TagSNP [31,120,180]

[Yung-Chien]

@hewm2008 ,

Oh yes I Found the parameter in the tutorial PDF, this is my personal negligence. Here is a final question, after finishing the analysis, I got a block like this: Could I quickly get the start and end position from the output files? It seems strange that I can not find the block length although the Documentation mentioned you can get the block_length in the "out.blocks.gz" file as below, Well here is my output block file, Thanks for your patient, Best Regards, Yung-Chien

[Yung-Chien]

@hewm2008 , Oh I think I know the reason why the block length information disappered. It may be caused by the Blocktype parameter, I selected the type 2 and this column did not show.

[hewm2008]

There are start and end points in the file, you can use these two coordinates to correlate to get the block length . zcat chrXXX.blocks.gz| awk '$3-$2>1000' |less -S

[hewm2008]

@Yung-Chien the 1.38 ver A. The 1.38 released today will already limit the largest canvas near （-ResizeH） B. perl ShowLDSVG -h and perl ShowLDSVG -MoreHelp you can see more help and para

[Yung-Chien]

@hewm2008 , Oh thanks u very much for updating a new version.

[hewm2008]

The program recommends that the number of snp should not exceed 1w, and it is best to control it at 5k sites Here I provide a script that randomly selects an snp every XXX bps 程序建议snp数不要超1w个，最好控制在5k个位点，在这我提供了一个每多少bp就随机挑一个snp的脚本：

#!/usr/bin/perl -w
use strict;

die  "Version 1.0\t2020-11-05;\nUsage: $0 \n" unless (@ARGV ==2);

my $InFile=$ARGV[0] ;
if  ($InFile =~s/\.gz$/\.gz/)
{
     open IA,"gzip -cd  $InFile | "  || die "input file can't open $!" ;
}
else
{
     open IA,"$InFile"  || die "input file can't open $!" ;
}
open (OA,">$ARGV[1]") || die "output file can't open $!" ;

my %hash=();
my $bin=5000;         #  可以修改 控制在1w左右 
my $column=1; 
my  $Num=1;
    while( < IA > )      ##    Remove spaces   IA    
    { 
        chomp ;
        if  ($_=~s/#/#/) 
        {
            print OA  $_,"\n";
                        next ;
        }
        my @inf=split ;
        my $site=int($inf[$column]/$bin);
        my $key=$inf[0]."_".$site;
        if (!exists $hash{$key})
        {
            print OA $_,"\n";
            $hash{$key}=1;
        }
        else
        {
            $hash{$key}++;
            if ($hash{$key}<=$Num)
            {
                print OA $_,"\n";
            }
        }

    }
close IA;
close OA ;

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