plotHighestExprs {scater} | R Documentation

## Plot the highest expressing features

### Description

Plot the features with the highest average expression across all cells, along with their expression in each individual cell.

### Usage

    plotHighestExprs(
      object,
      n = 50,
      colour_cells_by = NULL,
      drop_features = NULL,
      exprs_values = "counts",
      by_exprs_values = exprs_values,
      feature_names_to_plot = NULL,
      as_percentage = TRUE,
      swap_rownames = NULL
    )

### Arguments

`object` | A SingleCellExperiment object.
`n` | A numeric scalar specifying the number of the most expressed features to show.
`colour_cells_by` | Specification of a column metadata field or a feature to colour by, see `?retrieveCellInfo` for possible values.
`drop_features` | A character, logical or numeric vector indicating which features (e.g. genes, transcripts) to drop when producing the plot. For example, spike-in transcripts might be dropped to examine the contribution from endogenous genes.
`exprs_values` | A integer scalar or string specifying the assay to obtain expression values from.
`by_exprs_values` | A string or integer scalar specifying which assay to obtain expression values from, for use in colouring - see `?retrieveCellInfo` for details.
`feature_names_to_plot` | String specifying which row-level metadata column contains the feature names. Alternatively, an AsIs-wrapped vector or a data.frame, see `?retrieveFeatureInfo` for possible values. Default is `NULL`, in which case `rownames(object)` are used.
`as_percentage` | logical scalar indicating whether percentages should be plotted. If `FALSE`, the raw `exprs_values` are shown instead.
`swap_rownames` | Column name of `rowData(object)` to be used to identify features instead of `rownames(object)` when labelling plot elements.

### Details

This function will plot the percentage of counts accounted for by the top `n` most highly expressed features across the dataset. Each row on the plot corresponds to a feature and is sorted by average expression (denoted by the point). The distribution of expression across all cells is shown as tick marks for each feature. These ticks can be coloured according to cell-level metadata, as specified by `colour_cells_by`.

### Value

A ggplot object.

### Examples

    example_sce <- mockSCE()
    colData(example_sce) <- cbind(colData(example_sce),
         perCellQCMetrics(example_sce))

    plotHighestExprs(example_sce, colour_cells_by="detected")
    plotHighestExprs(example_sce, colour_cells_by="Mutation_Status")

[Package scater version 1.22.0 Index]