scater (version 1.0.4)

plotPhenoData: Plot phenotype data from an SCESet object

Description

Plot phenotype data from an SCESet object

Usage

plotPhenoData(object, aesth = aes_string(x = "log10(total_counts)", y = "total_features"), theme_size = 10, ...)

Arguments

object

an SCESet 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).

theme_size

numeric scalar giving default font size for plotting theme (default is 10).

...

arguments passed to plotMetadata.

Value

a ggplot plot object

Details

Plot phenotype data from an SCESet 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.

Examples

data("sc_example_counts")
data("sc_example_cell_info")
pd <- new("AnnotatedDataFrame", data = sc_example_cell_info)
example_sceset <- newSCESet(countData = sc_example_counts, phenoData = pd)
example_sceset <- calculateQCMetrics(example_sceset)
plotPhenoData(example_sceset, aesth = aes_string(x = "log10(total_counts)",
y = "total_features", colour = "Mutation_Status"))