Visualising features (eg gene expression), metadata (eg cell type) or reducedDim component (eg PhiSpace cell type score) in 2D tissue space.

The 2D spatial coordinates (x and y) should be stored as two columns in colData.

VizSpatial(
  obj,
  x_coord = "x",
  y_coord = "y",
  ptSize = 2,
  ptShape = 16,
  groupBy = NULL,
  feature = NULL,
  assay2use = NULL,
  reducedDim = NULL,
  reducedDim2use = "PhiSpace",
  censor = FALSE,
  quant = 0.5,
  legend.position = "right",
  legend.symb.size = NULL,
  legend.title = NULL,
  fsize = 14,
  reOrder = F,
  ...
)

Arguments

obj: Input object; either SingleCellExperiemnt or SpatialExperiment. If SingleCellExperiemnt, then colData(obj) has to contain columns named by x_coord and y_coord below.
x_coord: x coordinate name of a column of colData (if type(ojb) == SingleCellExperiemnt).
y_coord: y coordinate name of a column of colData (if type(ojb) == SingleCellExperiemnt).
ptSize: Size of point, representing spatial cell like objects (segmented cells, spots etc).
ptShape: Shape of point.
groupBy: Name of a metadata column to colour points by.
feature: Name of a feature (eg gene) to colour points by.
assay2use: Which assay to use when feature is specified.
reducedDim: Name of reducedDim column to colour points by.
reducedDim2use: Name of reducedDim layer to use when reducedDim is specified.
censor: Logical. Whether to set smaller colour values to zero. Default is FALSE. (Recommend to set to TRUE when visualise PhiSpace scores,)
quant: A value between 0 and 1. Colour values below quant will be set to zero if censor=TRUE.
legend.position: Position of legened, one of "right", "bottome", "left" and "top".
legend.symb.size: Legend symbol size (for discrete legend).
legend.title: Alternative legend name to replace the original.
fsize: Base font size of figure.
reOrder: Logical. Whether to reorder points according to their values (ascending) or not. Set to be TRUE to avoid overplotting.
...: Other arguments to pass to basicPlotFormat.

Value

A ggplot2 object.