Plot reduced dimensions. — plotDR • scider

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,
  pt.shape = 16,
  pt.size = 1,
  pt.alpha = 0.6,
  label = NULL,
  label.x = NULL,
  label.y = 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 polygons 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.
pt.shape: shape of points.
pt.size: size of points.
pt.alpha: alpha of points between 0 and 1.
label: label for the legend
label.x: label for the x-axis
label.y: 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

Value

A ggplot object.

Examples


data("xenium_bc_spe")
spe = runUMAP(spe)
#> Warning: PCA not found. Switching to counts assay instead.
plotDR(spe, group.by = "cell_type")