Plot specific reduced dimensions

Description

Wrapper functions to create plots for specific types of reduced dimension results in a SingleCellExperiment object, or, if they are not already present, to calculate those results and then plot them.

Usage

plotPCASCE(object, ..., rerun = FALSE, ncomponents = 2,
  run_args = list())

plotTSNE(object, ..., rerun = FALSE, ncomponents = 2,
  run_args = list())

plotUMAP(object, ..., rerun = FALSE, ncomponents = 2,
  run_args = list())

plotDiffusionMap(object, ..., rerun = FALSE, ncomponents = 2,
  run_args = list())

plotMDS(object, ..., rerun = FALSE, ncomponents = 2,
  run_args = list())

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

Arguments

Details

Each function will search the reducedDims slot for an appropriately named set of results and pass those coordinates onto plotReducedDim. If the results are not present or rerun=TRUE, they will be computed using the relevant run* function. The result name and run* function for each plot* function are:

• "PCA" and runPCA for plotPCA

• "TSNE" and runTSNE for plotTSNE

• "DiffusionMap" and runDiffusionMap for plotDiffusionMap

• "MDS" and runMDS for "plotMDS"

Users can specify arguments to the run* functions via run_args.

If ncomponents is a numeric vector, the maximum value will be used to determine the required number of dimensions to compute in the run* functions. However, only the specified dimensions in ncomponents will be plotted.

Value

A ggplot object.

Author(s)

Davis McCarthy, with modifications by Aaron Lun

See Also

runPCA, runDiffusionMap, runTSNE, runMDS, plotReducedDim

Examples

## Set up an example SingleCellExperiment
data("sc_example_counts")
data("sc_example_cell_info")
example_sce <- SingleCellExperiment(
    assays = list(counts = sc_example_counts), 
    colData = sc_example_cell_info
)
example_sce <- normalize(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")
plotPCA(example_sce, colour_by = "Cell_Cycle", shape_by = "Treatment",
    size_by = "Mutation_Status")

## Force legend to appear for shape:
example_subset <- example_sce[, example_sce$Treatment == "treat1"]
plotPCA(example_subset, colour_by = "Cell_Cycle", shape_by = "Treatment", 
    by_show_single = TRUE)

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

## Same for TSNE:
plotTSNE(example_sce, run_args=list(perplexity = 10))

## Same for DiffusionMaps:
plotDiffusionMap(example_sce)

## Same for MDS plots:
plotMDS(example_sce)