Difference between revisions of "MCScanX2figure"

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(mcscanx2figure.py)
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63:/data1/alima90/py/mcscanx2figure.py
 
63:/data1/alima90/py/mcscanx2figure.py
 
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[[File:88.svg|thumbnail]]
 
'''<big>Visualizing tool for MCScanX synteny block using SVG</big>
 
'''<big>Visualizing tool for MCScanX synteny block using SVG</big>
 
'''
 
'''
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highlight_link_opacity = 0.7
 
highlight_link_opacity = 0.7
 
 
 
 
  
 
== mcscanx2figure_schematic.py ==
 
== mcscanx2figure_schematic.py ==

Revision as of 04:03, 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:/data1/alima90/py/mcscanx2figure_schematic.py

Visualizing tool for MCScanX synteny block as schematic figure using SVG

README

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