Difference between revisions of "MCScanX2figure"

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Line 7: Line 7:
  
 
README
 
README
 +
 
command
 
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
 
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
 +
 
highlight_gene_list = ['geneA','geneB']
 
highlight_gene_list = ['geneA','geneB']
 +
 
You can also change color of element such as gene, link and backborn.
 
You can also change color of element such as gene, link and backborn.
 +
 
You can use RGB color as well as common color name
 
You can use RGB color as well as common color name
 +
  
  
 
=== USER SETTING PARAMETER ===
 
=== USER SETTING PARAMETER ===
 +
 
highlight_gene_list = ['Glyma12g04390']
 
highlight_gene_list = ['Glyma12g04390']
 +
 
backborn_color = 'rgb(135,206,250)'
 
backborn_color = 'rgb(135,206,250)'
 +
 
a_gene_color = 'blue'
 
a_gene_color = 'blue'
 +
 
b_gene_color = 'blue'
 
b_gene_color = 'blue'
 +
 
link_color = 'pink'
 
link_color = 'pink'
 +
 
link_opacity = 0.7
 
link_opacity = 0.7
 +
 
highlight_link_color = 'red'
 
highlight_link_color = 'red'
 +
 
highlight_link_opacity = 0.7
 
highlight_link_opacity = 0.7
  
Line 37: Line 52:
  
 
README
 
README
 +
 
command
 
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
 
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
 +
 
highlight_gene_list = ['geneA','geneB']
 
highlight_gene_list = ['geneA','geneB']
 +
 
You can also change color of element such as gene, link and backborn.
 
You can also change color of element such as gene, link and backborn.
 +
 
You can use RGB color as well as common color name
 
You can use RGB color as well as common color name
  
  
 
=== USER SETTING PARAMETER ===
 
=== USER SETTING PARAMETER ===
 +
 
highlight_gene_list = ['Glyma12g04390']
 
highlight_gene_list = ['Glyma12g04390']
 +
 
backborn_color = 'rgb(135,206,250)'
 
backborn_color = 'rgb(135,206,250)'
 +
 
gene_length = 10
 
gene_length = 10
 +
 
intergenic_scale = 5000 ## zoom out intergenic sequence scale into 1/x
 
intergenic_scale = 5000 ## zoom out intergenic sequence scale into 1/x
 +
 
a_gene_color = 'blue'
 
a_gene_color = 'blue'
 +
 
b_gene_color = 'blue'
 
b_gene_color = 'blue'
 +
 
link_color = 'pink'
 
link_color = 'pink'
 +
 
link_opacity = 0.7
 
link_opacity = 0.7
 +
 
highlight_link_color = 'red'
 
highlight_link_color = 'red'
 +
 
highlight_link_opacity = 0.7
 
highlight_link_opacity = 0.7

Revision as of 08:46, 11 April 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