README_go_plot.md

Plot the GO hierarchy with go_plot.py

• Plot six GO terms in a file (a different color for each) and their ancestors:
  • Using 'is_a' relationship only (default)
  • Using all relationships
• Plot one GO term and its ancestors:
  • Using 'is_a' relationship only (default)
  • Using all relationships
• Plot two GO terms and their ancestors:
  • Using 'is_a' relationship only (default)
  • Using all relationships
• Plot two GO terms (a different color for each) and their ancestors:
  • GO terms listed in a file
  • Using 'is_a' relationship only (default)
  • Using all relationships

Plot six GO terms (listed in a file) using different colors and their ancestors

The colorized GO terms use the colors from the lightbright color palette and an orange (#ffe5b4) from the favorite pink based oranges color palette.

The file, go_heartjogging6.txt, contains the GO terms and user-defined colors:

#fad2fa GO:0072359  # BP 643 D04 circulatory system development (magenta)
#d2fafa GO:0003007  # BP 197 D04 heart morphogenesis (blue)
#fafad2 GO:0035050  # BP  26 D05 embryonic heart tube development (yellow)
#ffe5b4 GO:0003304  # BP   0 D06 myocardial epithelial involution involved in heart jogging (orange)
#e6fad2 GO:0061371  # BP  11 D06 determination of heart left/right asymmetry (green)
#d2d2fa GO:0003146  # BP   6 D07 heart jogging (purple)

Six different-colored GO terms without relationships

The six GO IDs listed in go_heartjogging6.txt and their ancestors up to the root GO are plotted.

scripts/go_plot.py --go_file=tests/data/go_plot/go_heartjogging6.txt -o heartjogging6_r0.png

Six different-colored GO terms with relationships

The -r argument causes relationships to be plotted.

scripts/go_plot.py --go_file=tests/data/go_plot/go_heartjogging6.txt -r -o heartjogging6_r1.png

Plot one GO term and its ancestors

Plot one term and all ancestors using the 'is_a' attribute.

scripts/go_plot.py GO:0003304

Plot one GO term and its ancestors (with relationships)

Plot one term and all ancestors using the 'is_a' attribute and all relationships (--r).
The 'part_of' relationships are represented by dashed magenta arrows.

scripts/go_plot.py GO:0003304 --r

Plot two GO terms and their ancestors

Plot two terms and all ancestors using the 'is_a' attribute.

scripts/go_plot.py GO:0003304 GO:0003146 -o heart_jogging.png

Plot two GO terms and their ancestors (with relationships)

Plot two terms and all ancestors using the 'is_a' attribute and all relationships (--r).
The 'part_of' relationships are represented by dashed magenta arrows.

scripts/go_plot.py GO:0003304 GO:0003146 --r -o heart_jogging_r1.png

Plot two GO terms (listed in a file) using different colors and their ancestors

Plot two terms and all ancestors using the 'is_a' attribute. The heart jogging GO term, GO:0003146, is colored in ice.

The file, go_file1.txt, contains the GO terms and user-defined colors:

GO:0003304
GO:0003146 #d6fffa http://klaash.github.io/xkcdcolorpicker/#ice

scripts/go_plot.py --go_file=tests/data/go_plot/go_file1.txt -o heart_jogging_ice_gofile1.png

Plot two GO terms using different colors and their ancestors

Plot two terms and all ancestors using the 'is_a' attribute.
The heart jogging GO term, GO:0003146, is colored in ice.

scripts/go_plot.py GO:0003304 GO:0003146#d6fffa -o heart_jogging_ice.png

Plot two GO terms using different colors and their ancestors (with relationships)

Plot two terms ('heart jogging' (GO:0003146) colored in ice) and all ancestors using the 'is_a' attribute and all relationships (--r).
The 'part_of' relationships are represented by dashed magenta arrows.

scripts/go_plot.py GO:0003304 GO:0003146#d6fffa --r -o heart_jogging_ice_r1.png

Copyright (C) 2010-2018, DV Klopfenstein, Haibao Tang et al. All rights reserved.