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, or, if they are not already present, to calculate those results and then plot them.

Usage

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

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

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

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

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

Arguments

object

A SingleCellExperiment object.

...

Additional arguments to pass to plotReducedDim.

return_SCE

Logical, should the function return a SingleCellExperiment object with reduced dimension results in the reducedDim slot? Default is FALSE, in which case a ggplot object is returned. This will be deprecated in the next release in favour of directly calling the underlying run* functions to compute the results.

draw_plot

Logical, should the plot be drawn on the current graphics device? Only used if return_SCE is TRUE, otherwise the plot is always produced.

rerun

Logical, should the reduced dimensions be recomputed even if object contains an appropriately named set of results in the reducedDims slot?

ncomponents

Numeric scalar indicating the number of dimensions components to (calculate and) plot. This can also be a numeric vector, see ?plotReducedDim for details.

run_args

Arguments to pass to runPCA.

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:

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 or an SingleCellExperiment object, depending on return_SCE.

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, perplexity = 10)

## Same for DiffusionMaps:
plotDiffusionMap(example_sce)

## Same for MDS plots:
plotMDS(example_sce)
[Package scater version 1.8.4 Index]