Generate visualizations of CytoSPACER cell assignment results.
Usage
plot_cytospace(
results,
type = c("cell_types", "by_spot", "density"),
coordinates = NULL,
point_size = 1,
alpha = 0.8,
jitter = 0,
max_cells = 50000,
ncol = 3,
colors = NULL,
title = NULL
)Arguments
- results
Results from
run_cytospace.- type
Type of plot to generate:
- "cell_types"
Cell type spatial distribution (default)
- "by_spot"
Cell counts per spot, faceted by cell type
- "density"
Density of cell assignments
- coordinates
Optional coordinates data.frame.
- point_size
Size of points. Default is 1.
- alpha
Point transparency. Default is 0.8.
- jitter
Amount of jitter to add. Default is 0.
- max_cells
Maximum cells to plot. Default is 50000.
- ncol
Number of columns for faceted plots. Default is 3.
- colors
Named vector of colors per cell type.
- title
Plot title.
Examples
if (FALSE) { # \dontrun{
results <- run_cytospace(...)
plot_cytospace(results, type = "cell_types")
plot_cytospace(results, type = "cell_types", jitter = 0.3)
} # }