getCellsFromPolygon: Get cells located within the polygons area

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

Get cells located within the polygons area

Description

Get cells located within the polygons area

Usage

getCellsFromPolygon(
  gobject,
  polygon_name = "selections",
  spat_unit = "cell",
  spat_loc_name = "raw",
  polygons = NULL
)

Arguments

gobject	A Giotto object
polygon_name	name of polygon selections
spat_unit	spatial unit, default = 'cell'
spat_loc_name	name of spatial locations to use, default = 'raw'
polygons	character. A vector with polygon names to extract cells from. If NULL, cells from all polygons are retrieved

Value

A terra 'SpatVector' with cell ID, x y coordinates, and polygon ID where each cell is located in.

Examples

## Not run: 
## Plot interactive polygons
my_spatPlot <- spatPlot2D(gobject = my_giotto_object,
                          show_image = TRUE,
                          point_alpha = 0.75,
                          save_plot = FALSE)
my_polygon_coords <- plotInteractivePolygons(my_spatPlot)

## Add polygon coordinates to Giotto object
my_giotto_polygons <- createGiottoPolygonsFromDfr(my_polygon_coords)
my_giotto_object <- addGiottoPolygons(gobject = my_giotto_object,
                                      gpolygons = list(my_giotto_polygons))

## Get cells located within polygons area
getCellsFromPolygon(my_giotto_object)

## Get only cells from polygon 1
getCellsFromPolygon(my_giotto_object, polygons = "polygon 1")

## End(Not run)

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.