GeneSet Overlap Heatmap

Here we use a heatmap to visualize the overlap between gene sets within a single collection.

Plotting Guide Setup

A shared setup for all plotting guides.

# OS-independent path management.
from os import environ
from pathlib import Path
import numpy as np
import GSForge as gsf
import holoviews as hv
hv.extension('bokeh')

OSF_PATH = Path(environ.get("GSFORGE_DEMO_DATA", default="~/GSForge_demo_data/")).expanduser().joinpath("osfstorage", "oryza_sativa")
GEM_PATH = OSF_PATH.joinpath("AnnotatedGEMs", "oryza_sativa_hisat2_raw.nc")
LIT_DGE_GSC_PATH = OSF_PATH.joinpath("GeneSetCollections", "literature", "DGE")

agem = gsf.AnnotatedGEM(GEM_PATH)
agem

<GSForge.AnnotatedGEM>
Name: Oryza Sativa
Selected GEM Variable: 'counts'
    Gene   66338
    Sample 475

gsc = gsf.GeneSetCollection.from_folder(
    gem=agem, target_dir=LIT_DGE_GSC_PATH, name="DGE Results")
gsc

<GSForge.GeneSetCollection>
DGE Results
GeneSets (0 total): Support Count

Viewing GeneSet Overlaps within a GeneSetCollection

gsf.plots.collections.WithinCollectionOverlapHeatMap(gsc)