plotFeatureData {scater} | R Documentation

## Plot feature (gene) data from a SingleCellExperiment object

### Description

`plotFeatureData` and `plotRowData` are synonymous.

### Usage

    plotFeatureData(object, aesth = aes_string(x = "n_cells_counts", y =
      "log10_total_counts"), ...)

    plotRowData(...)

### Arguments

`object` | an `SingleCellExperiment` object containing expression values and experimental information. Must have been appropriately prepared.
`aesth` | aesthetics function call to pass to ggplot. This function expects at least x and y variables to be supplied. The default is to produce a density plot of number of cells expressing the feature (requires `calculateQCMetrics` to have been run on the `SingleCellExperiment` object prior).
`...` | arguments passed to `plotMetadata`, e.g. `theme_size`, `size`, `alpha`, `shape`.

### Details

Plot feature (gene) data from an SingleCellExperiment object. If one variable is supplied then a density plot will be returned. If both variables are continuous (numeric) then a scatter plot will be returned. If one variable is discrete and one continuous then a violin plot with jittered points overlaid will be returned. If both variables are discrete then a jitter plot will be produced. The object returned is a ggplot object, so further layers and plotting options (titles, facets, themes etc) can be added.

### 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 <- calculateQCMetrics(example_sce)
    plotFeatureData(example_sce, aesth = aes(x = n_cells_counts, y = log10_total_counts))

    plotRowData(example_sce, aesth = aes(x = n_cells_counts, y = log10_total_counts))

[Package scater version 1.6.3 Index]