goatools.godag_plot module

Plot a GODagSmall.

goatools.godag_plot.plot_gos(fout_png, goids, obo_dag, *args, **kws)

Given GO ids and the obo_dag, create a plot of paths from GO ids.

goatools.godag_plot.plot_goid2goobj(fout_png, goid2goobj, *args, **kws)

Given a dict containing GO id and its goobj, create a plot of paths from GO ids.

goatools.godag_plot.plot_results(fout_png, goea_results, *args, **kws)

Given a list of GOEA results, plot result GOs up to top.

goatools.godag_plot.plt_goea_results(fout_png, goea_results, *args, **kws)

Plot a single page.

class goatools.godag_plot.GODagPltVars

Bases: object

Holds plotting paramters.

rel2col = {'capable_of': 'dodgerblue', 'capable_of_part_of': 'darkorange', 'is_a': 'black', 'negatively_regulates': 'red', 'occurs_in': 'aquamarine4', 'part_of': 'blue', 'positively_regulates': 'green', 'regulates': 'gold'}

alpha2col = {0.005: 'mistyrose', 0.01: 'moccasin', 0.05: 'lemonchiffon1', 1.0: 'grey95'}

key2col = {'go_sources': 'palegreen', 'level_01': 'lightcyan'}

fmthdr = '{GO} L{level:>02} D{depth:>02}'

fmtres = '{study_count} genes'

items_p_line = 5

class goatools.godag_plot.GODagSmallPlot(godagsmall, *args, **kws)

Bases: object

Plot a graph contained in an object of type GODagSmall .

plt(fout_img, engine='pydot')

Plot using pydot, graphviz, or GML.