plotDimRedSCAtlasExperiment: Plot Dimensionality reductions of a Single-Cell Expression...

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

Plot Dimensionality reductions of a Single-Cell Expression Atlas experiment

Description

This function plots dimensionality reduction (PCA, t-sne, UMAP) of a SingleCellExperiment object representing a Single-Cell Expression Atlas experiment.

Usage

    plotDimRedSCAtlasExperiment( sceObject, dimRed, colorby )

Arguments

sceObject	Single-cell experiment object, representing a Single-Cell Expression Atlas experiment, obtained with the function getAtlasSCExperiment.
dimRed	Dimensionality reduction to plot. Options are: "X_pca", "X_tsne_perplexity_10", "X_umap_neighbors_20", etc.
colorby	Column name in colData to color the cells by.

Value

A ggplot2 geom point visualisation, which can be further customised by the user.

Examples

    # Example of plotting PCA dimensionality reduction colored by age

    # Download the experiment summary for E-ENAD-19
    enad19 <- getAtlasSCExperiment( "E-ENAD-19" )

    plotDimRedSCAtlasExperiment(enad19, dimRed = "X_pca", colorby = "age" )

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