plotColData {scater} | R Documentation

## Plot column metadata

### Description

Plot column-level (i.e., cell) metadata in an SingleCellExperiment object.

### Usage

    plotColData(object, y, x = NULL, colour_by = NULL, shape_by = NULL,
      size_by = NULL, by_exprs_values = "logcounts", by_show_single = FALSE,
      ...)

    plotPhenoData(...)

    plotCellData(...)

### Arguments

`object` | A SingleCellExperiment object containing expression values and experimental information.
`y` | Specification of the column-level metadata to show on the y-axis, see `?"scater-vis-var"` for possible values. Note that only metadata fields will be searched, `assays` will not be used.
`x` | Specification of the column-level metadata to show on the x-axis, see `?"scater-vis-var"` for possible values. Again, only metadata fields will be searched, `assays` will not be used.
`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.
`...` | Additional arguments for visualization, see `?"scater-plot-args"` for details.

### Details

If `y` is continuous and `x=NULL`, a violin plot is generated. If `x` is categorical, a grouped violin plot will be generated, with one violin for each level of `x`. If `x` is continuous, a scatter plot will be generated.

If `y` is categorical and `x` is continuous, horizontal violin plots will be generated. If `x` is missing or categorical, rectangule plots will be generated where the area of a rectangle is proportional to the number of points for a combination of factors.

Note that `plotPhenoData` and `plotCellData` are synonyms for `plotColData`. These are artifacts of the transition from the old SCESet class, and will be deprecated in future releases.

### 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 <- calculateQCMetrics(example_sce)
    example_sce <- normalize(example_sce)

    plotColData(example_sce, y = "total_features_by_counts",
       x = "log10_total_counts", colour_by = "Mutation_Status")

    plotColData(example_sce, y = "total_features_by_counts",
       x = "log10_total_counts", colour_by = "Mutation_Status",
       size_by = "Gene_0001", shape_by = "Treatment")

    plotColData(example_sce, y = "Treatment",
       x = "log10_total_counts", colour_by = "Mutation_Status")

    plotColData(example_sce, y = "total_features_by_counts",
       x = "Cell_Cycle", colour_by = "Mutation_Status")

[Package scater version 1.8.4 Index]