SketchKH

Distribution-Informed Sketching with Kernel Herding

Overview

We provide a set of functions for distribution-aware sketching of multiple profiled single-cell samples via Kernel Herding. Our sketches select a small, representative set of cells from each profiled sample so that all major immune cell-types and their relative frequencies are well-represented.

• Please see our paper for more information (ACM-BCB 2022) : https://arxiv.org/abs/2207.00584
• Updated : February 14, 2024

Installation

Dependencies

• Python >= 3.6, anndata >= 0.7.6, numpy >= 1.22.4, scipy >= 1.7.1, tqdm

You can install the package with pip by,

pip install sketchKH

Alternatively, you can clone the git repository by,

git clone https://github.com/CompCy-lab/SketchKH.git

Example usage

To perform sketching, first read in a preprocessed .h5ad adata object. This dataset contains multiple profiled single-cell samples. Hence, sketches will select a limited set of cells from each profiled sample. We refer to each profiled sample as a sample-set.

import anndata
import os
adata = anndata.read_h5ad(os.path.join('data', 'nk_cell_preprocessed.h5ad'))

Then simply sketch your data with 500 cells per sample-set by,

# Inputs
# adata: annotated data object (dimensions = cells x features)
# sample_set_key: string referring to the key within adata.obs that contains the sample-sets to subsample
# sample_set_inds: (alternative to specifying sample_set_key) list of arrays containing the indices of the sample-sets to subsample 
# gamma: scale parameter for the normal distribution standard deviation in random Fourier frequency feature computation
# frequency_seed: random state
# num_subsamples: number of cells to subsample per sample-set
# n_jobs: number of tasks
# ----------------------------

# Returns:
# kh_indices: list of indices referencing the subsampled cells per sample-set
# adata_subsample: downsampled annotated data object (dimensions = num_subsamples*sample-sets x features)

# ----------------------------
from sketchKH import *
kh_indices, adata_subsample = sketch(adata, sample_set_key = 'FCS_File', gamma = 1, num_subsamples = 500, frequency_seed = 0, n_jobs = -1)