Difference between revisions of "MCScanX2figure"

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README
 
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
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{| class="wikitable"
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|-
 +
! Header Command
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|-
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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
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|}
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 +
 
  
 
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
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README
 
README
  
command
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{| 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
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|}
  
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