Difference between revisions of "MCScanX2figure"
From Crop Genomics Lab.
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'''<big>Visualizing tool for MCScanX synteny block using SVG</big> | '''<big>Visualizing tool for MCScanX synteny block using SVG</big> | ||
''' | ''' | ||
− | + | [[File:Test1.PNG|frameless]] | |
README | README | ||
Revision as of 10:09, 10 October 2014
Contents |
mcscanx2figure.py
63:/data1/alima90/py/mcscanx2figure.py
Visualizing tool for MCScanX synteny block using SVG README
Command |
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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 |
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python mcscanx2figure_schematic.py config_file mcscanx_file(collinearity) block_number > output.svg |
Config file
MCScanX2figure_schematic config file example