plotHighestExprs: Plot the highest expressing features

Description Usage Arguments Details Value Examples

View source: R/plotHighestExprs.R

Description

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

Usage

1
2
3
4
plotHighestExprs(object, n = 50, controls, colour_cells_by,
  drop_features = NULL, exprs_values = "counts",
  by_exprs_values = exprs_values, by_show_single = TRUE,
  feature_names_to_plot = NULL, as_percentage = TRUE)

Arguments

object

A SingleCellExperiment object.

n

A numeric scalar specifying the number of the most expressed features to show.

controls

Specification of the row-level metadata column indicating whether a feature is a control, see ?"scater-vis-var" for possible values. Only metadata fields will be searched, assays will not be used. If not supplied, this defaults to "is_feature_control" or equivalent for compacted data.

colour_cells_by

Specification of a column metadata field or a feature to colour by, see ?"scater-vis-var" for possible values. If not supplied, this defaults to "total_features_by_counts" or equivalent for compacted data.

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 ?"scater-vis-var" for details.

by_show_single

Logical scalar specifying whether single-level factors should be used for colouring, see ?"scater-vis-var" for details. Default is NULL, in which case rownames(object) are used.

feature_names_to_plot

Specification of which row-level metadata column contains the feature names, see ?"scater-vis-var" for possible values.

as_percentage

logical scalar indicating whether percentages should be plotted. If FALSE, the raw exprs_values are shown instead.

Details

This function will plot the percentage of counts accounted for by the top n most highly expressed features across the dataset. Each feature corresponds to a row on the plot, sorted by average expression (denoted by the point).

The plot will attempt to colour the points based on whether the corresponding feature is labelled as a control in object. This can be turned off by setting controls=NULL.

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. Setting colour_cells_by=NULL will disable all tick colouring.

Value

A ggplot object.

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
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, 
    feature_controls = list(set1 = 1:500)
)

plotHighestExprs(example_sce, colour_cells_by ="total_features")
plotHighestExprs(example_sce, controls = NULL)
plotHighestExprs(example_sce, colour_cells_by="Mutation_Status")

scater documentation built on May 2, 2018, 3:36 a.m.