Difference between revisions of "MCScanX2figure"

Revision as of 05:15, 13 October 2014

63:/data1/alima90/py/mcscanx2figure.py

Visualizing tool for MCScanX synteny block using SVG

README

Command
python mcscanx2figure.py config_file mcscanx_file(collinearity) block_number > output.svg

63:/home/alima90/py/mcscanx2figure_schematic_v1.1.py

Visualizing tool for MCScanX synteny block as schematic figure using SVG

README

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

MCScanX2figure_schematic config file example

@@ Line 13: / Line 13: @@
 ! 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 config_file 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 ==