plotReducedDim: Plot reduced dimension representation of cells

In dynverse/scaterlegacy: Single-cell analysis toolkit for gene expression data in R

Description

Plot reduced dimension representation of cells

Usage

plotReducedDim(object, ...)

plotReducedDim.default(df_to_plot, ncomponents = 2, colour_by = NULL,
  shape_by = NULL, size_by = NULL, percentVar = NULL, theme_size = 10,
  legend = "auto")

plotReducedDim.SCESet(object, ncomponents = 2, colour_by = NULL,
  shape_by = NULL, size_by = NULL, exprs_values = "exprs",
  theme_size = 10, legend = "auto")

## S4 method for signature 'SCESet'
plotReducedDim(object, ncomponents = 2, colour_by = NULL,
  shape_by = NULL, size_by = NULL, exprs_values = "exprs",
  theme_size = 10, legend = "auto")

## S4 method for signature 'data.frame'
plotReducedDim(object, ncomponents = 2,
  colour_by = NULL, shape_by = NULL, size_by = NULL, percentVar = NULL,
  legend = "auto")

Arguments

object	an SCESet object with a non-NULL reducedDimension slot.
...	optional arguments (from those listed above) passed to plotReducedDim.SCESet or plotReducedDim.default
df_to_plot	data.frame containing a reduced dimension represenation of cells and optional metadata for the plot.
ncomponents	numeric scalar indicating the number of principal components to plot, starting from the first principal component. Default is 2. If ncomponents is 2, then a scatterplot of Dimension 2 vs Dimension 1 is produced. If ncomponents is greater than 2, a pairs plots for the top dimensions is produced.
colour_by	character string defining the column of pData(object) to be used as a factor by which to colour the points in the plot. Alternatively, a data frame with one column containing values to map to colours for all cells.
shape_by	character string defining the column of pData(object) to be used as a factor by which to define the shape of the points in the plot.
size_by	character string defining the column of pData(object) to be used as a factor by which to define the size of points in the plot.
percentVar	numeric vector giving the proportion of variance in expression explained by each reduced dimension. Only expected to be used internally in the plotPCA function.
theme_size	numeric scalar giving default font size for plotting theme (default is 10).
legend	character, specifying how the legend(s) be shown? Default is "auto", which hides legends that have only one level and shows others. Alternatives are "all" (show all legends) or "none" (hide all legends).
exprs_values	a string specifying the expression values to use for colouring the points, if colour_by or size_by are set as feature names.

Details

The function plotReducedDim.default assumes that the first ncomponents columns of df_to_plot contain the reduced dimension components to plot, and that any subsequent columns define factors for colour_by, shape_by and size_by in the plot.

Value

a ggplot plot object

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)
drop_genes <- apply(exprs(example_sceset), 1, function(x) {var(x) == 0})
example_sceset <- example_sceset[!drop_genes, ]

reducedDimension(example_sceset) <- prcomp(t(exprs(example_sceset)), scale. = TRUE)$x
plotReducedDim(example_sceset)
plotReducedDim(example_sceset, colour_by="Cell_Cycle")
plotReducedDim(example_sceset, colour_by="Cell_Cycle", shape_by="Treatment")
plotReducedDim(example_sceset, colour_by="Cell_Cycle", size_by="Treatment")
plotReducedDim(example_sceset, ncomponents=5)
plotReducedDim(example_sceset, ncomponents=5, colour_by="Cell_Cycle", shape_by="Treatment")
plotReducedDim(example_sceset, colour_by="Gene_0001")

dynverse/scaterlegacy documentation built on Feb. 17, 2020, 5:07 a.m.