cell_group: Add manual cell group labels to SingleCellExperiment
In jianhaizhang/spatialHeatmap: spatialHeatmap

cell_group

R Documentation

Add manual cell group labels to SingleCellExperiment

Description

Add manually created cell group labels in a data.frame to SingleCellExperiment.

Usage

cell_group(sce, df.group, cell, cell.group)

Arguments

`sce`	A `SingleCellExperiment`.
`df.group`	A `data.frame` of manually created single cell groups. At least two columns are required, corresponding to cell identifiers that are present in `rownames(colData(sce))` and the manually created group labels respectively.
`cell`	The column name in `df.group` indicating cells.
`cell.group`	The column name in `df.group` indicating cell group labels.

Value

An object of SingleCellExperiment.

Author(s)

Jianhai Zhang jzhan067@ucr.edu
Dr. Thomas Girke thomas.girke@ucr.edu

References

Morgan M, Obenchain V, Hester J, Pagès H (2022). SummarizedExperiment: SummarizedExperiment container. R package version 1.26.1, https://bioconductor.org/packages/SummarizedExperiment

Examples

set.seed(10); library(SummarizedExperiment)
# Read single cell data.
sce.pa <- system.file("extdata/shinyApp/data", "cell_mouse_brain.rds", package="spatialHeatmap")
sce <- readRDS(sce.pa)
# Quality control, normalization, dimensionality reduction on the single cell data.
sce.dimred <- process_cell_meta(sce, qc.metric=list(subsets=list(Mt=rowData(sce)$featureType=='mito'), threshold=1))
# Read manual cell group labels.
manual.clus.mus.sc.pa <- system.file("extdata/shinyApp/data", "manual_cluster_mouse_brain.txt", package="spatialHeatmap") 
manual.clus.mus.sc <- read.table(manual.clus.mus.sc.pa, header=TRUE, sep='\t')
# Include manual cell group labels in "SingleCellExperiment".
sce.clus <- cell_group(sce=sce.dimred, df.group=manual.clus.mus.sc, cell='cell', cell.group='cluster')

jianhaizhang/spatialHeatmap documentation built on July 31, 2024, 2:59 a.m.