In [1]:

    

import pyparanoid.genomeplot as gplot
%matplotlib inline


    

In [3]:

    

## Using the match_seqs function, or some other method you may have a list of groups
## you want to see mapped over a tree. For example...
!head ../src/all_groups.txt


    

    




group_01585	ColR
group_01909	ColS
group_03515	ArnC
group_03597	ArnA
group_00716	ArnB
group_03063	ArnT
group_03599	ArnF
group_03623	ArnE
group_03622	ArnD
group_02717	EptA

In [2]:

    

hm = gplot.plot_multigene_presence("../src/all_groups.txt","../../data/Pseudo" \
                              ,"../src/exp_strains.rerooted.tre",outfile="test")


    

In [4]:

    

## This heatmap is ordered from top to bottom based on the branching pattern of the tree.
## Thus, you can combine the heatmap with a tree to make a publication-quality image in Illustrator.