chrVis is a chromosome visualization tool, aims to facilitate the identification and analysis of linkage blocks, chromosome structure and differences from comparisons of chromosomes. Our tool is effective in displaying variation in chromosome structure and, generally, any other kind of positional blocks on the chromosome intervals.
- Image auto Size
- Legend support
- Block name auto arrangement
- Symbols or glyph mark support
- Links between chromosomes
- Tutorials and Samples
The script requires python module : svgwrite
install with pip:
pip install svgwrite`
python App.py --conf sample.conf --out sample_out.svg
usage: App.py [-h] [-c CONF] [-o OUT]
optional arguments:
-h, --help show this help message and exit
-c CONF, --conf CONF configure file
-o OUT, --out OUT output filename
[general]
karyotype = sample_chr.txt
bandfile = sample_gene.txt
scale = 50000
imgWidth = 1200
imgHeight = 600
[ideogram]
thickness = 20
spacing = 80
fill = yes
label_size = 20
[band]
alpha = 1
thickness = 10
show_name = True
Three columns chromosome ID,chromesome name , chromosome length, chromosome color
chr1 My.Chr1 28954470 #333300
chr2 My.Chr2 30652350 #333300
chr3 My.Chr3 25211582 #333300
chr4 My.Chr4 29556843 #333300
chr5 My.Chr5 24787886 #333300
chr6 My.Chr6 22802870 #333300
chr7 My.Chr7 11041128 #333300
chr8 My.Chr8 18570557 #333300
chr9 My.Chr9 28466655 #333300
chr10 My.Chr10 17444910 #333300
chr11 My.Chr11 18674527 #333300
chr12 My.Chr12 23362826 #333300
chr13 My.Chr13 19446246 #333300
Five columns chromosome name , band name,band start,band end, fill color
chr1 block0 18655440 19004551 #bacac6
chr4 block63 21300577 21681252 #bacac6
chr4 block64 19835040 21134129 #bacac6
chr4 block65 24342697 25086406 #00bc12
chr5 block73 15698017 17228364 #00bc12
chr5 block74 19286756 20060843 #00bc12
chr5 block75 14726663 15515996 #00bc12
chr5 block76 18302344 19240018 #00bc12
chr5 block77 20273832 20935547 #00bc12
chr10 block11 0 17444910 #0eb83a
chr6 block84 2855768 3460898 #0eb83a
chr8 block91 10654172 11720140 #0eb83a
chr8 block92 11768805 12802006 #0eb83a
chr8 block93 10394348 10605509 #0eb83a
chr11 block18 14537869 15203608 #16a951
chr3 block55 10019219 11003401 #16a951
chr6 block85 16028585 17345205 #16a951
chr4 block66 13980220 14717750 #f35336
chr4 block67 13448043 13874835 #f35336
chr4 block68 12779674 13388859 #f35336
chr9 block96 13165043 14384072 #f35336
chr9 block97 11152423 12218998 #f35336
chr9 block98 12392176 13083726 #f35336
React
Typescript
Django
Laravel
Facebook
Microsoft
Google
Alibaba
D3
Tencent