R: Plot reduced dimensions

plotReducedDim {scater}

R Documentation

Plot reduced dimensions

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(),
  ...
)

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.
`...`	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")

[Package scater version 1.16.2 Index]