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Plot dimensional reduction categorical variables

Source: R/VizMethods.R
PlotDimRed.Rd

Plot categorical variables in dimensional reduction.

Usage

PlotDimRed.SingleCellExperiment(
  object,
  color.by,
  dimred,
  dims,
  use.color,
  point.size,
  point.stroke,
  legend.nrow,
  seed.color,
  label,
  plot.theme,
  rasterise,
  rasterise.dpi,
  legend.justification,
  legend.size,
  legend.title
)

# S4 method for class 'SingleCellExperiment'
PlotDimRed(
  object,
  color.by,
  dimred = tail(reducedDimNames(object), n = 1),
  dims = 1:2,
  use.color = NULL,
  point.size = 1,
  point.stroke = 1,
  legend.nrow = 2,
  seed.color = 123,
  label = FALSE,
  plot.theme = theme_classic(),
  rasterise = (ncol(object) <= 30000),
  rasterise.dpi = 300,
  legend.justification = "center",
  legend.size = 10,
  legend.title = color.by
)

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.

dims

Dimensions from the dimensional reduction embedding to plot.

use.color

Character specifying the colors. By default NULL, i.e., colors are randomly chosen based on the seed given at seed.color.

point.size

Size of points. By default 1.

point.stroke

Size of stroke. By default 1.

legend.nrow

Display legend items by this number of rows. By default 2.

seed.color

Seed to randomly select colors. By default 123.

label

Logical to add or not categorical labels to the centroid categories. By default FALSE, i.e., labels are not added.

plot.theme

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

rasterise

Logical specifying if points should be rasterised or not. By default TRUE, if more than 3e4 cells, otherwise FALSE.

rasterise.dpi

In case rasterise = TRUE, DPI to use. By default 300.

legend.justification

Legend justification. By default "center".

legend.size

Legend size. By default 10

legend.title

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

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 batch 
PlotDimRed(object = sce, color.by = "Batch", dimred = "PCA", legend.nrow = 1)


# Plot cell type annotations
PlotDimRed(object = sce, color.by = "Species", legend.nrow = 1, 
          dimred = "PCA", label = TRUE)
#> Warning: Removed 147 rows containing missing values or values outside the scale range
#> (`geom_text_repel()`).