plotMDS {scater} | R Documentation |
#' Produce an MDS plot from the cell pairwise distance data in an
SingleCellExperiment
dataset.
plotMDS(object, ncomponents = 2, colour_by = NULL, shape_by = NULL, size_by = NULL, return_SCE = FALSE, rerun = FALSE, draw_plot = TRUE, exprs_values = "logcounts", theme_size = 10, legend = "auto", ...)
object |
an |
ncomponents |
numeric scalar indicating the number of principal
components to plot, starting from the first principal component. Default is
2. If |
colour_by |
character string defining the column of |
shape_by |
character string defining the column of |
size_by |
character string defining the column of |
return_SCE |
logical, should the function return an |
rerun |
logical, should PCA be recomputed even if |
draw_plot |
logical, should the plot be drawn on the current graphics
device? Only used if |
exprs_values |
a string specifying the expression values to use for
colouring the points, if |
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
|
... |
arguments passed to S4 plotMDS method |
The function cmdscale
is used internally to
compute the multidimensional scaling components to plot.
If return_SCE
is TRUE
, then the function returns an
SingleCellExperiment
object, otherwise it returns a ggplot
object.
## Set up an example SingleCellExperiment data("sc_example_counts") data("sc_example_cell_info") example_sce <- SingleCellExperiment( assays = list(counts = sc_example_counts), colData = sc_example_cell_info) example_sce <- normalize(example_sce) drop_genes <- apply(exprs(example_sce), 1, function(x) {var(x) == 0}) example_sce <- example_sce[!drop_genes, ] ## Examples plotting plotMDS(example_sce) plotMDS(example_sce, colour_by = "Cell_Cycle") plotMDS(example_sce, colour_by = "Cell_Cycle", shape_by = "Treatment") ## define cell-cell distances differently plotMDS(example_sce, colour_by = "Cell_Cycle", shape_by = "Treatment", size_by = "Mutation_Status", method = "canberra")