readH5ADObsVar: Extract a variable from adata.obs stored in an H5AD file

In CytoSimplex: Simplex Visualization of Cell Fate Similarity in Single-Cell Data

Extract a variable from adata.obs stored in an H5AD file

Description

Primarily designed for fetching the annotation used for visualization.

Usage

readH5ADObsVar(filename, obsKey, named = TRUE, categoricalAsFactor = TRUE)

Arguments

filename	File path to the H5AD file.
obsKey	The variable name to extract, must use only one character string.
named	Logical, whether to name the vector with cell IDs that came from adata.obs_names. Default TRUE.
categoricalAsFactor	Logical, whether to convert categorical variables to factors. Default TRUE.

Value

A vector of the extracted variable, or a factor if the variable is encoded to be categorical and categoricalAsFactor = TRUE.

See Also

Other H5AD-reader: readH5ADObsNames(), readH5ADUnsSpMat(), readVelocytoLoom()

Examples

## Not run: 
h5adFile <- "path/to/analysis.h5ad"
cluster <- readH5ADObsVar(h5adFile, "leiden")

## End(Not run)

CytoSimplex documentation built on June 8, 2025, 10:12 a.m.