GeneSet Overlap Heatmaps¶

Plotting Guide Setup

In [1]:

import os
import numpy as np

import holoviews as hv
hv.extension('bokeh')

import GSForge as gsf

Declare used paths

In [2]:

# OS-independent path management.
from os import fspath, environ
from pathlib import Path

In [3]:

OSF_PATH = Path(environ.get("GSFORGE_DEMO_DATA", default="~/GSForge_demo_data")).expanduser()
AGEM_PATH = OSF_PATH.joinpath("osfstorage", "rice.nc")
BOR_COLL_PATH = OSF_PATH.joinpath("osfstorage", "boruta_gene_sets")
assert AGEM_PATH.exists()

Load an AnnotatedGEM

In [4]:

agem = gsf.AnnotatedGEM(AGEM_PATH)
agem

Out[4]:

<GSForge.AnnotatedGEM>
Name: Rice
Selected GEM Variable: 'counts'
    Gene   55986
    Sample 475

In [5]:

gsc = gsf.GeneSetCollection.from_folder(gem=agem, target_dir=BOR_COLL_PATH, 
                                        name="Boruta Results")
gsc

Out[5]:

<GSForge.GeneSetCollection>
Boruta Results
GeneSets (3 total): Support Count
    Boruta_Treatment: 681
    Boruta_Genotype: 661
    Boruta_Subspecies: 231

Viewing GeneSet Overlaps¶

In [6]:

gsf.plots.geneset_overlap_heatmap(gsc).opts(
    width=300, height=300, xrotation=90, xlabel="", ylabel="")

Out[6]:

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