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]