Difference between revisions of "MCScanX2figure"
(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 | |
− | + | 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'] | 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 | |
− | + | 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'] | 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 | ||
− |
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