plotReducedDim: Plot reduced dimensions

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

Description

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

Usage

plotReducedDim(
  object,
  dimred,
  ncomponents = 2,
  percentVar = NULL,
  colour_by = NULL,
  shape_by = NULL,
  size_by = NULL,
  by_exprs_values = "logcounts",
  text_by = NULL,
  text_size = 5,
  text_colour = "black",
  label_format = c("%s %i", " (%i%%)"),
  other_fields = list(),
  swap_rownames = NULL,
  ...
)

Arguments

object	A SingleCellExperiment object.
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 the by argument in ?retrieveCellInfo for possible values.
shape_by	Specification of a column metadata field or a feature to shape by, see the by argument in ?retrieveCellInfo for possible values.
size_by	Specification of a column metadata field or a feature to size by, see the by argument in ?retrieveCellInfo 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 the exprs_values argument in ?retrieveCellInfo.
text_by	String specifying the column metadata field with which to add text labels on the plot. This must refer to a categorical field, i.e., coercible into a factor. Alternatively, an AsIs vector or data.frame, see ?retrieveCellInfo.
text_size	Numeric scalar specifying the size of added text.
text_colour	String specifying the colour of the added text.
label_format	Character vector of length 2 containing format strings to use for the axis labels. The first string expects a string containing the result type (e.g., "PCA") and an integer containing the component number, while the second string shows the rounded percentage of variance explained and is only relevant when this information is provided in object.
other_fields	Additional cell-based fields to include in the data.frame, see ?"scater-plot-args" for details.
swap_rownames	Column name of rowData(object) to be used to identify features instead of rownames(object) when labelling plot elements.
...	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

example_sce <- mockSCE()
example_sce <- logNormCounts(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")

scater documentation built on Feb. 28, 2021, 2:01 a.m.