createGiottoPolygonsFromMask: Create giotto polygons from mask file
In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

createGiottoPolygonsFromMask

R Documentation

Create giotto polygons from mask file

Description

Creates Giotto polygon object from a mask file (e.g. segmentation results)

Usage

createGiottoPolygonsFromMask(
  maskfile,
  mask_method = c("guess", "single", "multiple"),
  name = "cell",
  remove_background_polygon = FALSE,
  background_algo = c("range"),
  fill_holes = TRUE,
  poly_IDs = NULL,
  flip_vertical = TRUE,
  shift_vertical_step = TRUE,
  flip_horizontal = TRUE,
  shift_horizontal_step = TRUE,
  calc_centroids = FALSE,
  fix_multipart = TRUE,
  remove_unvalid_polygons = TRUE
)

Arguments

`maskfile`	path to mask file
`mask_method`	how the mask file defines individual segmentation annotations
`name`	name for polygons
`remove_background_polygon`	try to remove background polygon (default: FALSE)
`background_algo`	algorithm to remove background polygon
`fill_holes`	fill holes within created polygons
`poly_IDs`	unique names for each polygon in the mask file
`flip_vertical`	flip mask figure in a vertical manner
`shift_vertical_step`	shift vertical (boolean or numerical)
`flip_horizontal`	flip mask figure in a horizontal manner
`shift_horizontal_step`	shift horizontal (boolean or numerical)
`calc_centroids`	calculate centroids for polygons
`fix_multipart`	try to split polygons with multiple parts (default: TRUE)
`remove_unvalid_polygons`	remove unvalid polygons (default: TRUE)