Reduced dimension plots {scater} | R Documentation

## 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)

    plotTSNE(object, ..., ncomponents = 2)

    plotUMAP(object, ..., ncomponents = 2)

    plotDiffusionMap(object, ..., ncomponents = 2)

    plotMDS(object, ..., ncomponents = 2)

    plotNMF(object, ..., ncomponents = 2)

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

### 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.

### 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")

    ## Same for DiffusionMaps:
    example_sce <- runDiffusionMap(example_sce)
    plotDiffusionMap(example_sce)

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

[Package scater version 1.16.2 Index]