Plot cells based on spatial coordinates.

Usage

plotSpatial(
  spe,
  group.by = NULL,
  feature = NULL,
  assay = "counts",
  type = c("log", "raw", "cpm", "logcpm"),
  cols = NULL,
  highlight = NULL,
  cols.highlight = NULL,
  pt.shape = 16,
  pt.size = 0.3,
  pt.size.highlight = 1,
  pt.alpha = 1,
  label = NULL,
  cols.scale = NULL,
  reverseY = NULL,
  image = FALSE,
  ncol = NULL,
  per.scale = TRUE,
  range = NULL,
  transform = "identity",
  ...
)

Arguments

spe

A SpatialExperiment object.

group.by

values to group points by. Must be in colData of spe. If NULL, will try with 'cols' if available.

feature

Feature(s) to colour points by; must be in rownames(spe). If a vector of more than one feature is supplied, one panel is drawn per feature (see per.scale, ncol), as in Seurat::FeaturePlot.

assay

Name of assay to use for plotting feature.

type

Transformation to apply for the group/feature. Options are "raw" , "log", "cpm", "logcpm", or a function that accepts and returns a vector of the same length. For feature plots the legend title defaults to the matching unit ("Counts", "log2 Cts", "CPM", "log2-CPM"); for a single feature the gene name becomes the plot title. Override the legend with label.

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

cols.scale

vector of position for color if colors should not be evenly positioned. See scale_color_gradientn. Only applicable for continuous values.

reverseY

Logical. Whether to reverse Y coordinates. Default is TRUE if the spe contains an image (even if not plotted) and FALSE if otherwise.

image

Logical. Whether to draw the background tissue image (forwarded to plotImage). Default FALSE.

ncol

Number of columns when plotting multiple features. Passed to facet_wrap (shared scale) or wrap_plots (per-panel scales). Default NULL lets the layout be chosen automatically.

per.scale

Logical. For multiple features, whether each panel gets its own colour scale (TRUE, default; like Seurat::FeaturePlot, via the 'patchwork' package; the image is drawn in every panel) or a single shared colour scale across panels (FALSE).

range

Numeric length-2 (lower, upper) cap for continuous colour values

a single feature, or multiple features with a shared scale; values outside are clamped. A single value is taken as the upper bound. Default NULL (no capping). Ignored when per.scale = TRUE (each panel auto-scales).

transform

Name of a transformation for the continuous colour scale (e.g. "log10", "log1p", "pseudo_log", "sqrt"), passed to scale_color_gradientn; the colour spectrum is spaced by the transform while the legend stays in original units. Default "identity" (no transformation). Use "log10" for nicely log-spaced legend breaks (needs positive values); "log1p"/"pseudo_log" tolerate zeros but keep linear breaks. Only affects continuous (feature or numeric group.by) colouring. Use "log10" for log-spaced legend breaks (requires positive values); "log1p"/"pseudo_log" tolerate zeros but keep linear breaks.

...

Parameters pass to plotImage

Value

A ggplot object.

Examples


data("xenium_bc_spe")

plotSpatial(spe, group.by = "cell_type", pt.size = 0.5, pt.alpha = 0.6)