dotPlotSCAtlasExperiment: Dot-plot for a 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

Dot-plot for a Single-Cell Expression Atlas experiment

Description

This function generates a Dot-Plot from a SingleCellExperiment object coming from a Single-Cell Expression Atlas experiment.

Usage

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

Arguments

singleCellExperiment	A SingleCellExperiment object from Single Cell Expression Atlas
genes	Vector of gene IDs to include in the dot-plot.
sel.K	Number of clusters for Single Cell Expression Atlas Experiment. If both sel.K is NULL, the function will use default clustering 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.

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" )

    dotPlotSCAtlasExperiment(egeod6552, genes=c('ENSG00000166681','ENSG00000178928', 'ENSG00000142182' , 'ENSG00000160282' ), sel.K=4)

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