Difference between revisions of "MCScanX2figure"
(→mcscanx2figure_schematic.py) |
(→mcscanx2figure_schematic.py) |
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== mcscanx2figure_schematic.py == | == mcscanx2figure_schematic.py == | ||
− | 63:/ | + | 63:/home/alima90/py/mcscanx2figure_schematic_v1.1.py |
'''<big>Visualizing tool for MCScanX synteny block as schematic figure using SVG</big> | '''<big>Visualizing tool for MCScanX synteny block as schematic figure using SVG</big> | ||
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! Command | ! Command | ||
|- | |- | ||
− | | python mcscanx2figure_schematic.py | + | | python mcscanx2figure_schematic.py config_file mcscanx_file(collinearity) block_number > output.svg |
|} | |} | ||
− | + | === Config file === | |
− | + | left_species_gff_file_path = Brapa_197_gene.gff3.sort | |
− | + | right_species_gff_file_path = Thalophila_173_gene.gff3.sort | |
− | + | highlight_gene_list = Bra002260,Bra002261 | |
− | + | highlight_link_list = None | |
− | + | backborn_color = rgb(135,206,250) | |
− | + | ||
− | + | ||
− | + | ||
− | === | + | |
− | + | ||
− | highlight_gene_list = | + | |
− | + | ||
− | backborn_color = | + | |
− | + | ||
gene_length = 10 | gene_length = 10 | ||
− | + | ## intergenic_scale : zoom out intergenic sequence scale into 1/x | |
− | + | intergenic_scale = 1000 | |
− | + | arrow_size = 5 | |
− | a_gene_color = | + | a_gene_color = blue |
− | + | highlight_a_gene_color = red | |
− | b_gene_color = | + | b_gene_color = blue |
− | + | highlight_b_gene_color = red | |
− | link_color = | + | link_color = pink |
− | + | link_opacity = 0.5 | |
− | link_opacity = 0. | + | highlight_link_color = red |
− | + | highlight_link_opacity = 0.8 | |
− | highlight_link_color = | + | |
− | + | ||
− | highlight_link_opacity = 0. | + |
Revision as of 10:03, 10 October 2014
Contents |
mcscanx2figure.py
63:/data1/alima90/py/mcscanx2figure.py
Visualizing tool for MCScanX synteny block using SVG
README
Command |
---|
python mcscanx2figure.py gff_file_of_left_species_in_mcscanx gff_file_of_right_species_in_mcscanx mcscanx_file(collinearity) block_number > output.svg |
if you want to highlight link, add your genes in highlight_gene_list like
highlight_gene_list = ['geneA','geneB']
You can also change color of element such as gene, link and backborn.
You can use RGB color as well as common color name
USER SETTING PARAMETER
highlight_gene_list = ['Glyma12g04390']
backborn_color = 'rgb(135,206,250)'
a_gene_color = 'blue'
b_gene_color = 'blue'
link_color = 'pink'
link_opacity = 0.7
highlight_link_color = 'red'
highlight_link_opacity = 0.7
mcscanx2figure_schematic.py
63:/home/alima90/py/mcscanx2figure_schematic_v1.1.py
Visualizing tool for MCScanX synteny block as schematic figure using SVG
README
Command |
---|
python mcscanx2figure_schematic.py config_file mcscanx_file(collinearity) block_number > output.svg |
Config file
left_species_gff_file_path = Brapa_197_gene.gff3.sort right_species_gff_file_path = Thalophila_173_gene.gff3.sort highlight_gene_list = Bra002260,Bra002261 highlight_link_list = None backborn_color = rgb(135,206,250) gene_length = 10
- intergenic_scale : zoom out intergenic sequence scale into 1/x
intergenic_scale = 1000 arrow_size = 5 a_gene_color = blue highlight_a_gene_color = red b_gene_color = blue highlight_b_gene_color = red link_color = pink link_opacity = 0.5 highlight_link_color = red highlight_link_opacity = 0.8