valency-anndata 0.1.1

Experimental tooling to support notebook analysis of polislike data

valency-anndata

Experimental tooling to support notebook analysis of polislike data.

:sparkles: Inspired by scanpy and the scverse ecosystem! :heart:

Installation

pip install valency-anndata

Usage

Loading Polis Data

import valency_anndata as val

adata = val.datasets.polis.load("https://pol.is/report/r29kkytnipymd3exbynkd")
val.viz.schematic_diagram(adata, diff_from=None)

Running Polis Pipelines

with val.viz.schematic_diagram(diff_from=adata):
    val.tools.recipe_polis(adata, key_added_pca="X_pca_polis")

val.viz.embedding(adata, basis="pca_polis", color="kmeans_polis")

Exploring Polis Pipelines

val.viz.schematic_diagram(diff_from=adata):
    val.preprocessing.calculate_qc_metrics(pacmap_adata, inplace=True)

val.viz.embedding(adata, basis="pca_polis",
    color=["kmeans_polis", "pct_seen", "pct_agree", "pct_pass"],
)

Running & Exploring Alternative Pipelines

from valency_anndata.tools._polis import _zero_mask, _cluster_mask

with val.viz.schematic_diagram(diff_from=adata):
    _zero_mask(adata)
    val.preprocessing.impute(
        adata,
        strategy="mean",
        source_layer="X_masked",
        target_layer="X_masked_imputed_mean",
    )
    val.tools.pacmap(
        adata,
        key_added="X_pacmap",
        layer="X_masked_imputed_mean",
    )
    _cluster_mask(adata)
    val.tools.kmeans(
        adata,
        k_bounds=(2, 9),
        use_rep="X_pacmap",
        mask_obs="cluster_mask",
        key_added="kmeans_pacmap",
    )

val.viz.embedding(adata, basis="pacmap",
    color=["kmeans_pacmap", "pct_seen", "pct_agree", "pct_pass"],
)

For full examples and planned features, see: example-usage.ipynb

Contributing

We are maintaining a custom CONTRIBUTING.md with specific links and a compiled list of entry tasks!