plotReducedDim {scater}R Documentation

Plot reduced dimensions

Description

Plot cell-level reduced dimension results stored in a SingleCellExperiment object.

Usage

plotReducedDim(object, use_dimred, ncomponents = 2, percentVar = NULL,
  colour_by = NULL, shape_by = NULL, size_by = NULL,
  by_exprs_values = "logcounts", by_show_single = FALSE,
  text_by = NULL, text_size = 5, text_colour = "black", ...)

Arguments

object

A SingleCellExperiment object.

use_dimred

A string or integer scalar indicating the reduced dimension result in reducedDims(object) to plot.

ncomponents

A numeric scalar indicating the number of dimensions to plot, starting from the first dimension. Alternatively, a numeric vector specifying the dimensions to be plotted.

percentVar

A numeric vector giving the proportion of variance in expression explained by each reduced dimension. Only expected to be used in PCA settings, e.g., in the plotPCA function.

colour_by

Specification of a column metadata field or a feature to colour by, see ?"scater-vis-var" for possible values.

shape_by

Specification of a column metadata field or a feature to shape by, see ?"scater-vis-var" for possible values.

size_by

Specification of a column metadata field or a feature to size by, see ?"scater-vis-var" for possible values.

by_exprs_values

A string or integer scalar specifying which assay to obtain expression values from, for use in point aesthetics - see ?"scater-vis-var" for details.

by_show_single

Logical scalar specifying whether single-level factors should be used for point aesthetics, see ?"scater-vis-var" for details.

text_by

Specification of a column metadata field for which to add text - see ?"scater-vis-var" for possible values. This must refer to a categorical field, i.e., coercible into a factor.

text_size

Numeric scalar specifying the size of added text.

text_colour

String specifying the colour of the added text.

...

Additional arguments for visualization, see ?"scater-plot-args" for details.

Details

If ncomponents is a scalar equal to 2, a scatterplot of the first two dimensions is produced. If ncomponents is greater than 2, a pairs plots for the top dimensions is produced.

Alternatively, if ncomponents is a vector of length 2, a scatterplot of the two specified dimensions is produced. If it is of length greater than 2, a pairs plot is produced containing all pairwise plots between the specified dimensions.

The text_by option will add factor levels as labels onto the plot, placed at the median coordinate across all points in that level. This is useful for annotating position-related metadata (e.g., clusters) when there are too many levels to distinguish by colour. It is only available for scatterplots.

Value

A ggplot object

Author(s)

Davis McCarthy, with modifications by Aaron Lun

Examples

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)

example_sce <- runPCA(example_sce, ncomponents=5)
plotReducedDim(example_sce, "PCA")
plotReducedDim(example_sce, "PCA", colour_by="Cell_Cycle")
plotReducedDim(example_sce, "PCA", colour_by="Gene_0001")

plotReducedDim(example_sce, "PCA", ncomponents=5)
plotReducedDim(example_sce, "PCA", ncomponents=5, colour_by="Cell_Cycle", 
    shape_by="Treatment")


[Package scater version 1.12.2 Index]