plotMDS: Produce a multidimensional scaling plot for an SCESet object

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

Description

#' Produce an MDS plot from the cell pairwise distance data in an SCESet dataset.

Usage

plotMDS(object, ...)

plotMDSSCESet(object, ncomponents = 2, colour_by = NULL, shape_by = NULL,
  size_by = NULL, return_SCESet = FALSE, draw_plot = TRUE,
  exprs_values = "exprs", theme_size = 10, legend = "auto")

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

Arguments

object	an SCESet object
...	arguments passed to S4 plotMDS method
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 PC2 vs PC1 is produced. If ncomponents is greater than 2, a pairs plots for the top components is produced. NB: computing more than two components for t-SNE can become very time consuming.
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.
return_SCESet	logical, should the function return an SCESet object with principal component values for cells in the reducedDimension slot. Default is FALSE, in which case a ggplot object is returned.
draw_plot	logical, should the plot be drawn on the current graphics device? Only used if return_SCESet is TRUE, otherwise the plot is always produced.
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.
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).

Details

The function cmdscale is used internally to compute the multidimensional scaling components to plot.

Value

If return_SCESet is TRUE, then the function returns an SCESet object, otherwise it returns a ggplot object.

Examples

## Set up an example SCESet
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, ]
example_sceset <- calculateQCMetrics(example_sceset)

## define cell-cell distances
cellDist(example_sceset) <- as.matrix(dist(t(exprs(example_sceset))))

## Examples plotting
plotMDS(example_sceset)
plotMDS(example_sceset, colour_by = "Cell_Cycle")
plotMDS(example_sceset, colour_by = "Cell_Cycle",
shape_by = "Treatment")

## define cell-cell distances differently
cellDist(example_sceset) <- as.matrix(dist(t(counts(example_sceset)),
method = "canberra"))
plotMDS(example_sceset, colour_by = "Cell_Cycle",
shape_by = "Treatment", size_by = "Mutation_Status")

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