GEM Rasters

Here we display gene intensity values as an image. Using the datashader library, we can create a dynamic raster of the entire GEM.

Specific results from this plot are not the goal, rather hope to not see strange patterns in expression or missing values that may indicate a problem in a previous processing step.

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")
TOUR_BORUTA = OSF_PATH.joinpath("GeneSetCollections", "tour_boruta")

echo $GSFORGE_DEMO_DATA

  File "/tmp/ipykernel_5532/3939668663.py", line 1
    echo $GSFORGE_DEMO_DATA
         ^
SyntaxError: invalid syntax

ls $GSFORGE_DEMO_DATA

ls $GSFORGE_DEMO_DATA/AnnotatedGEMs

agem = gsf.AnnotatedGEM(GEM_PATH)
agem

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

Creating a Count Matrix Raster

gsf.plots.gem.RasterGEM(agem)

Selecting a GeneSet from a collection provides a raster of just those supported genes.

gsf.plots.gem.RasterGEM(gsc, selected_gene_sets=["Boruta_treatment"], hue="genotype")