layer_territory: layer_territory generates layer from the outside to the...

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

layer_territory generates layer from the outside to the inside of a territory

Description

layer_territory generates layer from the outside to the inside of a territory

Usage

layer_territory(
  vesalius_assay,
  territory = NULL,
  trial = "last",
  layer_depth = NULL,
  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
layer_depth	integer describing the number of final layers.
morphology_factor	integer or vector of integers describing growth and/or shrink extent.
verbose	logical - progress message output.

Details

Each territory can be subdivided into a series of layers. Each layer will be considered a seperate territory and can be treated as such for functions such as identify_markers and territory_plot.

However, all other territories present will be labled as "out". This means that for the time being you can only work with a single territory at a time.

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 <- layer_territory(ves)

# view territory morphing
territory_plot(ves)

## End(Not run)

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