The sifter

This tutorial shows how to use the sifter() function to apply SiFT with a single function call.

We use the Drosophila wing disc development single cell data [1] for the demonstration.

[1] Everetts, N. J., Worley, M. I., Yasutomi, R., Yosef, N., & Hariharan, I. K. (2021). Single-cell transcriptomics of the Drosophila wing disc reveals instructive epithelium-to-myoblast interactions. Elife, 10, e61276.

import scanpy as sc

import sift

Import data

download pre-processed data drosopila.annotated.h5ad

DATA_DIR = ".../drosophila.annotated.h5ad"  # set path to anndata

adata = sc.read(DATA_DIR)

Run sifter

We apply filtering using a mapping kernel (metric="mapping") defined with respect to cell cycle and sex labels (kernel_key="phase_sex") and filtering the gene expression (embedding_key="X").

Additional parameters we can specify are:

• copy: bool stating whether the adata is modified in place or copied.

• pseudocount: add a pseudocount to the filtered object to ensure non-negativity of X.

metric_ = "mapping"
kernel_key_ = "phase_sex"
embedding_key_ = "X"

sift.sifter(
    adata=adata,
    kernel_key=kernel_key_,
    metric=metric_,
    embedding_key=embedding_key_,
    copy=False,
    pseudocount=False,
)

INFO     sift: initialized a SiFTer with mapping kernel.
INFO     sift: Filtering cell-cell similarity kernel using projection on `X`.
INFO     sift: The data is `SiFTed`!
         The filtered embedding is stored in `adata.X`
             Finish

Visualize results

We observe the removal of the nuisance effect with respect to the cell cycle, sex, cc \& sex labels along-with the marker genes PCNA (cell cycle marker), and lncRNA:roX1 (sex marker).

Further, for a biological marker gene, Nrt, we see a pattern is preserved.

sc.tl.pca(adata)
sc.pp.neighbors(adata)
sc.tl.umap(adata)

sc.pl.umap(
    adata,
    color=["phase", "sex", "phase_sex", "PCNA", "lncRNA:roX1", "Nrt"],
    title=[
        "cell cycle phase",
        "sex",
        "cc phase & sex",
        "PCNA\n(cc marker)",
        "lncRNA:roX1\n(sex marker)",
        "Nrt\n(biological marker)",
    ],
    frameon=False,
    wspace=0.1,
    ncols=3,
)