scater (version 1.0.4)

plotMetadata: Plot metadata for cells or features

Description

Plot metadata for cells or features

Usage

plotMetadata(object, aesth = aes_string(x = "log10(total_counts)", y = "total_features"), shape = NULL, alpha = NULL, size = NULL, theme_size = 10)

Arguments

object

a data.frame (or object that can be coerced to such) object containing metadata in columns to plot.

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).

shape

numeric scalar to define the plotting shape. Ignored if shape is included in the aesth argument.

alpha

numeric scalar (in the interval 0 to 1) to define the alpha level (transparency) of plotted points. Ignored if alpha is included in the aesth argument.

size

numeric scalar to define the plotting size. Ignored if size is included in the aesth argument.

theme_size

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

Value

a ggplot plot object

Details

Plot cell or feature metadata 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)
plotMetadata(pData(example_sceset))