Plot cells based on spatial coordinates.
Usage
plotSpatial(
spe,
reverseY = FALSE,
group.by = NULL,
feature = NULL,
assay = "counts",
type = c("raw", "log", "cpm", "logcpm"),
cols = NULL,
pt.shape = 16,
pt.size = 0.3,
pt.alpha = 0.5,
label = NULL,
cols.scale = NULL
)Arguments
- spe
A SpatialExperiment object.
- reverseY
Reverse y coordinates.
- 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.
- 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.
- 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
- cols.scale
vector of position for color if colors should not be evenly positioned. See scale_color_gradientn. Only applicable for continuous values.
Examples
data("xenium_bc_spe")
plotSpatial(spe, group.by = "cell_type", pt.size = 0.5, pt.alpha = 0.6)
