plotReducedDim {scater} | R Documentation

## Plot reduced dimension representation of cells

### Description

Plot reduced dimension representation of cells

### Usage

    plotReducedDimDefault(df_to_plot, ncomponents = 2, percentVar = NULL,
      colour_by = NULL, shape_by = NULL, size_by = NULL, theme_size = 10,
      legend = "auto")

    plotReducedDim(object, use_dimred, ncomponents = 2, colour_by = NULL,
      shape_by = NULL, size_by = NULL, exprs_values = "logcounts",
      percentVar = NULL, ...)

### Arguments

`df_to_plot` | data.frame containing a reduced dimension represenation of cells and optional metadata for the plot.
`ncomponents` | numeric scalar indicating the number of principal components to plot, starting from the first principal component. Default is 2. If `ncomponents` is 2, then a scatterplot of Dimension 2 vs Dimension 1 is produced. If `ncomponents` is greater than 2, a pairs plots for the top dimensions is produced.
`percentVar` | numeric vector giving the proportion of variance in expression explained by each reduced dimension. Only expected to be used internally in the `plotPCA` function.
`colour_by` | character string defining the column of `pData(object)` to be used as a factor by which to colour the points in the plot. Alternatively, a data frame with one column containing values to map to colours for all cells.
`shape_by` | character string defining the column of `pData(object)` to be used as a factor by which to define the shape of the points in the plot.
`size_by` | character string defining the column of `pData(object)` to be used as a factor by which to define the size of points in the plot.
`theme_size` | numeric scalar giving default font size for plotting theme (default is 10).
`legend` | character, specifying how the legend(s) be shown? Default is `"auto"`, which hides legends that have only one level and shows others. Alternatives are "all" (show all legends) or "none" (hide all legends).
`object` | an `SingleCellExperiment` object with a non-NULL `reducedDimension` slot.
`use_dimred` | character, name of reduced dimension representation of cells stored in `SingleCellExperiment` object to plot (e.g. "PCA", "TSNE", etc).
`exprs_values` | a string specifying the expression values to use for colouring the points, if `colour_by` or `size_by` are set as feature names.
`...` | optional arguments (from those listed above) passed to `plotReducedDimDefault`

### Details

The function `plotReducedDim.default` assumes that the first `ncomponents` columns of `df_to_plot` contain the reduced dimension components to plot, and that any subsequent columns define factors for `colour_by`, `shape_by` and `size_by` in the plot.

### Value

a ggplot plot object

### 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)
    drop_genes <- apply(exprs(example_sce), 1, function(x) {var(x) == 0})
    example_sce <- example_sce[!drop_genes, ]

    reducedDim(example_sce, "PCA") <- prcomp(t(exprs(example_sce)), scale. = TRUE)$x
    plotReducedDim(example_sce, "PCA")
    plotReducedDim(example_sce, "PCA", colour_by="Cell_Cycle")
    plotReducedDim(example_sce, "PCA", colour_by="Cell_Cycle", shape_by="Treatment")
    plotReducedDim(example_sce, "PCA", colour_by="Cell_Cycle", size_by="Treatment")
    plotReducedDim(example_sce, "PCA", ncomponents=5)
    plotReducedDim(example_sce, "PCA", ncomponents=5, colour_by="Cell_Cycle", shape_by="Treatment")
    plotReducedDim(example_sce, "PCA", colour_by="Gene_0001")

[Package scater version 1.6.3 Index]