plotPhenoData {scater}R Documentation

Plot cell phenotype data from an SingleCellExperiment object

Description

plotPhenoData, plotColData and plotCellData are synonymous.

Usage

plotPhenoData(object, aesth = aes_string(x = "log10(total_counts)", y =
  "total_features"), ...)

plotColData(...)

plotCellData(...)

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 plot total_features against log10(total_counts).

...

arguments passed to plotPhenoData (if plotColData or plotCellData) or to plotMetadata, e.g.theme_size, size, alpha, shape.

Details

Plot phenotype data from a 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)
plotPhenoData(example_sce, aesth = aes_string(x = "log10(total_counts)",
y = "total_features", colour = "Mutation_Status"))

plotColData(example_sce, aesth = aes_string(x = "log10(total_counts)",
y = "total_features", colour = "Mutation_Status"))

plotCellData(example_sce, aesth = aes_string(x = "log10(total_counts)",
y = "total_features", colour = "Mutation_Status"))


[Package scater version 1.6.3 Index]