Difference between revisions of "MCScanX2figure"
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README | README | ||
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command | command | ||
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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 | 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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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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highlight_gene_list = ['geneA','geneB'] | highlight_gene_list = ['geneA','geneB'] | ||
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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. | ||
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You can use RGB color as well as common color name | You can use RGB color as well as common color name | ||
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=== USER SETTING PARAMETER === | === USER SETTING PARAMETER === | ||
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highlight_gene_list = ['Glyma12g04390'] | highlight_gene_list = ['Glyma12g04390'] | ||
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backborn_color = 'rgb(135,206,250)' | backborn_color = 'rgb(135,206,250)' | ||
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a_gene_color = 'blue' | a_gene_color = 'blue' | ||
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b_gene_color = 'blue' | b_gene_color = 'blue' | ||
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link_color = 'pink' | link_color = 'pink' | ||
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link_opacity = 0.7 | link_opacity = 0.7 | ||
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highlight_link_color = 'red' | highlight_link_color = 'red' | ||
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highlight_link_opacity = 0.7 | highlight_link_opacity = 0.7 | ||
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README | README | ||
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command | command | ||
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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 | 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