plotDR is the main function for plotting reduced dimension. Others are wrapper functions for convenience.
Usage
plotDR(
spe,
dimred = NULL,
dims = c(1, 2),
group.by = NULL,
feature = NULL,
assay = "counts",
cols = NULL,
highlight = NULL,
cols.highlight = NULL,
pt.shape = 16,
pt.size = 0.7,
pt.size.highlight = 1,
pt.alpha = 0.6,
label = NULL,
xlab = NULL,
ylab = NULL,
cols.scale = NULL
)
plotUMAP(spe, dimred = "UMAP", ...)
plotPCA(spe, dimred = "PCA", ...)Arguments
- spe
A SpatialExperiment object.
- dimred
Name of the reduced dimension in reducedDims
- dims
Numeric vector length 2 for the dimensions to be plotted. Default to first two dimensions
- group.by
values to group points by. Must be in colData of spe. If NULL, will try with 'cols' if available.
- feature
Feature to group points by. Must be in rownames(spe).
- assay
Name of assay to use for plotting feature.
- cols
Colour palette. Can be a vector of colours or a function that accepts an integer n and return n colours.
- highlight
Optional cells to emphasise, given as either a vector of group.by levels (characters or cluster numbers), or a logical vector of length ncol(spe) selecting cells directly. Highlighted cells are drawn last (on top) at pt.size.highlight; all other cells are light grey at pt.size.
- cols.highlight
Colour(s) for the highlighted cells. Defaults to NULL, which keeps each level's usual group.by palette colour. A single colour (e.g. "red") colours all highlighted cells the same; a vector matching the number of 'highlight' entries gives one colour per level (matched by position).
- pt.shape
shape of points.
- pt.size
size of points.
- pt.size.highlight
size of highlighted points (see highlight).
- pt.alpha
alpha of points between 0 and 1.
- label
label for the legend
- xlab
label for the x-axis
- ylab
label for the y-axis
- cols.scale
vector of position for color if colors should not be evenly positioned. See scale_color_gradientn. Only applicable for continuous values.
- ...
Additional arguments pass to plotDR
