heatmapSCAtlasExperiment: Visualise heatmap for Single-Cell Expression Atlas experiment

In ebi-gene-expression-group/bioconductor-ExpressionAtlas: Search, download and visualise datasets from EMBL-EBI Expression Atlas and Single-Cell Expression Atlas

Visualise heatmap for Single-Cell Expression Atlas experiment

Description

This function plots a heatmap from a SingleCellExperiment object coming from a Single-Cell Expression Atlas experiment.

Usage

    heatmapSCAtlasExperiment( singleCellExperiment, genes=NULL, sel.K=NULL, scaleNormExp=FALSE, show_row_names=FALSE )

Arguments

singleCellExperiment	A SingleCellExperiment object from Single Cell Expression Atlas
genes	Vector of gene IDs to include in the heatmap. If NULL, all genes will be shown for the default clustering. Default is NULL.
sel.K	Number of clusters for Single Cell Expression Atlas Experiment. If NULL, a gene list must be provided. If both sel.K and genes are NULL, the function will use default clustering for all markers genes for this experiment.
scaleNormExp	Logical indicating whether to scale normalized expression values, which adjusts the data to have a mean of zero and a standard deviation of one. Default is FALSE.
show_row_names	Logical indicating whether to show gene names in rows. Default is FALSE.

Value

A Heatmap-class object from the ComplexHeatmap package. This object can be further customized or combined with other heatmaps using the ComplexHeatmap package's functions.

Examples

    
    egeod6552 <- getAtlasSCExperiment( "E-GEOD-36552" )

    heatmap6552 <- heatmapSCAtlasExperiment( egeod6552, genes=NULL, sel.K=NULL, scaleNormExp=FALSE, show_row_names=FALSE )

    # Example with a specific gene list
    heatmap6552_genes <- heatmapSCAtlasExperiment( egeod6552, genes=c('ENSG00000151611','ENSG00000020577', 'ENSG00000188869' ), sel.K=NULL, scaleNormExp=FALSE, show_row_names=TRUE )

ebi-gene-expression-group/bioconductor-ExpressionAtlas documentation built on July 4, 2025, 12:53 a.m.