Difference between revisions of "MCScanX2figure"
Line 8: | Line 8: | ||
README | README | ||
− | |||
− | python mcscanx2figure.py gff_file_of_left_species_in_mcscanx gff_file_of_right_species_in_mcscanx mcscanx_file(collinearity) block_number > output.svg | + | {| class="wikitable" |
+ | |- | ||
+ | ! Header 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 | if you want to highlight link, add your genes in highlight_gene_list like | ||
Line 53: | Line 59: | ||
README | README | ||
− | + | {| class="wikitable" | |
+ | |- | ||
+ | ! Header Command | ||
+ | |- | ||
+ | | python mcscanx2figure_schematic.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 | if you want to highlight link, add your genes in highlight_gene_list like |
Revision as of 08:50, 11 April 2014
Contents |
mcscanx2figure.py
63:/data1/alima90/py/mcscanx2figure.py
Visualizing tool for MCScanX synteny block using SVG
README
Header 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:/data1/alima90/py/mcscanx2figure_schematic.py
Visualizing tool for MCScanX synteny block as schematic figure using SVG
README
Header Command |
---|
python mcscanx2figure_schematic.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)'
gene_length = 10
intergenic_scale = 5000 ## zoom out intergenic sequence scale into 1/x
a_gene_color = 'blue'
b_gene_color = 'blue'
link_color = 'pink'
link_opacity = 0.7
highlight_link_color = 'red'
highlight_link_opacity = 0.7