plot_reddim: Plot specific reduced dimensions

In LTLA/scater: Single-Cell Analysis Toolkit for Gene Expression Data in R

Plot specific reduced dimensions

Description

Wrapper functions to create plots for specific types of reduced dimension results in a SingleCellExperiment object.

Usage

plotPCASCE(object, ..., ncomponents = 2, dimred = "PCA")

plotTSNE(object, ..., ncomponents = 2, dimred = "TSNE")

plotUMAP(object, ..., ncomponents = 2, dimred = "UMAP")

plotDiffusionMap(object, ..., ncomponents = 2, dimred = "DiffusionMap")

plotMDS(object, ..., ncomponents = 2, dimred = "MDS")

plotNMF(object, ..., ncomponents = 2, dimred = "NMF")

## S4 method for signature 'SingleCellExperiment'
plotPCA(object, ..., ncomponents = 2, dimred = "PCA")

Arguments

object	A SingleCellExperiment object.
...	Additional arguments to pass to plotReducedDim.
ncomponents	Numeric scalar indicating the number of dimensions components to (calculate and) plot. This can also be a numeric vector, see ?plotReducedDim for details.
dimred	A string or integer scalar indicating the reduced dimension result in reducedDims(object) to plot.

Details

Each function is a convenient wrapper around plotReducedDim that searches the reducedDims slot for an appropriately named dimensionality reduction result:

• "PCA" for plotPCA

• "TSNE" for plotTSNE

• "DiffusionMap" for plotDiffusionMap

• "MDS" for "plotMDS"

• "NMF" for "plotNMF"

• "UMAP" for "plotUMAP"

Its only purpose is to streamline workflows to avoid the need to specify the dimred argument.

Value

A ggplot object.

Author(s)

Davis McCarthy, with modifications by Aaron Lun

See Also

runPCA, runDiffusionMap, runTSNE, runMDS, runNMF, and runUMAP, for the functions that actually perform the calculations.

plotReducedDim, for the underlying plotting function.

Examples

example_sce <- mockSCE()
example_sce <- logNormCounts(example_sce)
example_sce <- runPCA(example_sce)

## Examples plotting PC1 and PC2
plotPCA(example_sce)
plotPCA(example_sce, colour_by = "Cell_Cycle")
plotPCA(example_sce, colour_by = "Cell_Cycle", shape_by = "Treatment")

## Examples plotting more than 2 PCs
plotPCA(example_sce, ncomponents = 4, colour_by = "Treatment",
    shape_by = "Mutation_Status")

## Same for TSNE:
example_sce <- runTSNE(example_sce)
plotTSNE(example_sce, colour_by="Mutation_Status")

## Not run: 
## Same for DiffusionMaps:
example_sce <- runDiffusionMap(example_sce)
plotDiffusionMap(example_sce)

## End(Not run)

## Same for MDS plots:
example_sce <- runMDS(example_sce)
plotMDS(example_sce)

LTLA/scater documentation built on Feb. 7, 2024, 2:54 a.m.