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# 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.

```{code-cell} ipython3
# 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")
```

```{code-cell} ipython3
agem = gsf.AnnotatedGEM(GEM_PATH)
agem
```

```{code-cell} ipython3
gsc = gsf.GeneSetCollection.from_folder(
    gem=agem, target_dir=LIT_DGE_GSC_PATH, name="DGE Results")
gsc
```

## Viewing GeneSet Overlaps within a GeneSetCollection

```{code-cell} ipython3
gsf.plots.collections.WithinCollectionOverlapHeatMap(gsc)
```

```{code-cell} ipython3

```