Difference between revisions of "MCScanX2figure"

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(Created page with "== mcscanx2figure.py == 63:/data1/alima90/py/mcscanx2figure.py '''<big>Visualizing tool for MCScanX synteny block using SVG</big> ''' ##README ##command ##python mcscanx2fi...")
 
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'''
 
'''
  
##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
  
  
#3################################# 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)'
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highlight_link_color = 'red'
 
highlight_link_color = 'red'
 
highlight_link_opacity = 0.7
 
highlight_link_opacity = 0.7
##################################################################################
+
 
  
  
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'''
 
'''
  
##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 use RGB color as well as common color name
  
  
#3################################# 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)'
Line 55: Line 56:
 
highlight_link_color = 'red'
 
highlight_link_color = 'red'
 
highlight_link_opacity = 0.7
 
highlight_link_opacity = 0.7
##################################################################################
 

Revision as of 08:45, 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