plotFeatureData: Plot feature (gene) data from a SingleCellExperiment object

Description Usage Arguments Details Value Examples

View source: R/plotting.R

Description

plotFeatureData and plotRowData are synonymous.

Usage

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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

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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))

scater documentation built on Dec. 5, 2017, 2 a.m.