sketchData: Downsampling single cell data using geometric sketching...

In sqjin/CellChat: Inference and analysis of cell-cell communication from single-cell and spatial transcriptomics data

Downsampling single cell data using geometric sketching algorithm

Description

USERs need to install the python package 'pip install geosketch' (https://github.com/brianhie/geosketch)

Usage

sketchData(object, percent, idents = NULL, do.PCA = TRUE, dimPC = 30)

Arguments

object	A data matrix (should have row names; samples in rows, features in columns) or a Seurat object. When object is a PCA or UMAP space, please set 'do.PCA = FALSE' When object is a data matrix (cells in rows and genes in columns), it is better to use the highly variable genes. PCA will be done on this input data matrix.
percent	the percent of data to sketch
idents	A vector of identity classes to keep for sketching
do.PCA	whether doing PCA on the input data
dimPC	the number of components to use

Value

A vector of cell names to use for downsampling

sqjin/CellChat documentation built on Nov. 10, 2023, 4:29 a.m.