Difference between revisions of "MCScanX2figure"

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(mcscanx2figure_schematic.py)
(mcscanx2figure_schematic.py)
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== mcscanx2figure_schematic.py ==
 
== mcscanx2figure_schematic.py ==
  
63:/data1/alima90/py/mcscanx2figure_schematic_v1.1.py
+
63:/home/alima90/py/mcscanx2figure_schematic_v1.1.py
  
 
'''<big>Visualizing tool for MCScanX synteny block as schematic figure using SVG</big>
 
'''<big>Visualizing tool for MCScanX synteny block as schematic figure using SVG</big>
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! 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
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| python mcscanx2figure_schematic.py config_file mcscanx_file(collinearity) block_number > output.svg
 
|}
 
|}
  
  
if you want to highlight link, add your genes in highlight_gene_list like
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=== Config file ===
 
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left_species_gff_file_path = Brapa_197_gene.gff3.sort
highlight_gene_list = ['geneA','geneB']
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right_species_gff_file_path = Thalophila_173_gene.gff3.sort
 
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highlight_gene_list = Bra002260,Bra002261
You can also change color of element such as gene, link and backborn.
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highlight_link_list = None
 
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backborn_color = rgb(135,206,250)
You can use RGB color as well as common color name
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=== USER SETTING PARAMETER ===
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highlight_gene_list = ['Glyma12g04390']
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backborn_color = 'rgb(135,206,250)'
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gene_length = 10
 
gene_length = 10
 
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## intergenic_scale : zoom out intergenic sequence scale into 1/x
intergenic_scale = 5000 ## zoom out intergenic sequence scale into 1/x
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intergenic_scale = 1000
 
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arrow_size = 5
a_gene_color = 'blue'
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a_gene_color = blue
 
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highlight_a_gene_color = red
b_gene_color = 'blue'
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b_gene_color = blue
 
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highlight_b_gene_color = red
link_color = 'pink'
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link_color = pink
 
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link_opacity = 0.5
link_opacity = 0.7
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highlight_link_color = red
 
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highlight_link_opacity = 0.8
highlight_link_color = 'red'
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highlight_link_opacity = 0.7
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Revision as of 10:03, 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:/home/alima90/py/mcscanx2figure_schematic_v1.1.py

Visualizing tool for MCScanX synteny block as schematic figure using SVG

Mc2fc1.png

README

Command
python mcscanx2figure_schematic.py config_file mcscanx_file(collinearity) block_number > output.svg


Config file

left_species_gff_file_path = Brapa_197_gene.gff3.sort right_species_gff_file_path = Thalophila_173_gene.gff3.sort highlight_gene_list = Bra002260,Bra002261 highlight_link_list = None backborn_color = rgb(135,206,250) gene_length = 10

    1. intergenic_scale : zoom out intergenic sequence scale into 1/x

intergenic_scale = 1000 arrow_size = 5 a_gene_color = blue highlight_a_gene_color = red b_gene_color = blue highlight_b_gene_color = red link_color = pink link_opacity = 0.5 highlight_link_color = red highlight_link_opacity = 0.8