territory_morphing: territory_morphing applies morphological operators to a set...

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

territory_morphing applies morphological operators to a set of territoriees

Description

territory_morphing applies morphological operators to a set of territoriees

Usage

territory_morphing(
  vesalius_assay,
  territory = NULL,
  trial = "last",
  morphology_factor = 0,
  verbose = TRUE
)

Arguments

vesalius_assay	vesalius_assay object
territory	integer or vector of integers desrcining territories to morph.
trial	character string - which territory trial that should be used to select territorires. Default is last one computed
morphology_factor	integer or vector of integers describing growth and/or shrink extent.
verbose	logical - progress message output.

Details

Territory morphing can manipulate territories by growing, shrinking, filling, and cleaning territories. Growing = Positive integers - Territory will be dilated by x number of pixels Shrinking = Negative integers - Territory will be contracted by x number of pixels Filling = grow followed by shrink. Cleaning = shrink followed by grow.

Value

a vesalius_assay

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)

# morph territory

ves <- territory_morphing(ves, 8, morphology_factor = 30)
ves <- terriotry_morphing(ves, 1, morpholgy_factor = c(-15, 15))

# view territory morphing
territory_plot(ves)

## End(Not run)

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