territory_plot: territory_plot - plotting Vesalius territories

In patrickCNMartin/Vesalius: Vesalius: Dissecting Tissue Anatomy from Spatial Transcriptomic Data

territory_plot - plotting Vesalius territories

Description

territory_plot - plotting Vesalius territories

Usage

territory_plot(
  vesalius_assay,
  trial = "last",
  split = FALSE,
  highlight = NULL,
  contour = "None",
  randomise = TRUE,
  cex = 10,
  cex_pt = 1,
  alpha = 0.65,
  use_image = FALSE
)

Arguments

vesalius_assay	a vesalius_Assay object
trial	character string describing which segmentation trial to use. Default is "last" which is the last segmentation trial used.
split	logical - If TRUE, territories will be plotted in separate panels
highlight	numeric vector describing which territories should be highlighted.
contour	if territory contours should be added. Availble: "None", "convex", "concave"
randomise	logical - If TRUE, colour palette will be randomised.
cex	numeric describing font size multiplier.
cex_pt	numeric describing point size multiplier.
alpha	opacity factor ]0,1[

Details

Territory plots show all territories in false colour after they have been isolated from a Vesalius image.

Note that this function can be applied to image segments, territories, and layers.

Value

a ggplot object

Examples

## Not run: 
data(vesalius)
# First we build a simple object
ves <- build_vesalius_object(coordinates, counts)
# We can do a simple run
ves <- build_vesalius_embeddings(ves)

# simple smoothing
ves <- smooth_image(ves, dimensions = seq(1, 30))

# quick segmentation
ves <- segment_image(ves, dimensions = seq(1, 30))

# isolate territories
ves <- isolate_territories(ves)

# Plot Territories
p <- territory_plot(ves)

## End(Not run)

patrickCNMartin/Vesalius documentation built on April 17, 2025, 11:31 p.m.