Plot dimensional reduction feature expression

Plot feature expression in dimensional reduction.

Usage

PlotExpression.SingleCellExperiment(
  object,
  color.by,
  dimred,
  scale.values,
  color.scale,
  plot.theme,
  legend.title,
  point.size,
  point.stroke
)

# S4 method for class 'SingleCellExperiment'
PlotExpression(
  object,
  color.by,
  dimred = tail(reducedDimNames(object), n = 1),
  scale.values = FALSE,
  color.scale = "inferno",
  plot.theme = theme_classic(),
  legend.title = color.by,
  point.size = 1,
  point.stroke = 1
)

Arguments

object

An object of SingleCellExperiment class.

color.by

Categorical variable available in colData(object) to plot.

dimred

Dimensional reduction available in ReducedDimNames(object) to plot. By default the last dimensional reduction in the object is used.

scale.values

Logical specifying if values should be scaled. By default FALSE, i.e., values are not scaled.

color.scale

Character of color scale palette to be passed to ggplot2::scale_color_viridis_c. By default inferno. Other palettes are also available such as viridis.

plot.theme

Plot theme available in ggplot2. By default theme_classic().

legend.title

Legend title. By default the same as given at color.by.

point.size

Size of points. By default 1.

point.stroke

Size of stroke. By default 1.

Value

A plot of class ggplot.

Examples

# Import package
suppressPackageStartupMessages(library("SingleCellExperiment"))

# Create toy SCE data
batches <- c("b1", "b2")
set.seed(239)
batch <- sample(x = batches, size = nrow(iris), replace = TRUE)
sce <- SingleCellExperiment(assays = list(logcounts = t(iris[,1:4])),  
                           colData = DataFrame("Species" = iris$Species, 
                                             "Batch" = batch))
colnames(sce) <- paste0("samp", 1:ncol(sce))

# Compute dimensional reduction 
sce <- RunPCA(object = sce, assay.name = "logcounts", p = 4, 
           pca.method = "stats")

# Plot expression level of one or more features
## one 
PlotExpression(object = sce, color.by = "Petal.Width")


## more than one
features <- row.names(sce)[1:4] 
exp.plots <- lapply(X = features, FUN = function(x) {
    PlotExpression(object = sce, color.by = x, scale.values = TRUE)
})
cowplot::plot_grid(plotlist = exp.plots, ncol = 2, align = "vh")