addPolygonCells: Add corresponding polygon IDs to cell metadata

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

Add corresponding polygon IDs to cell metadata

Description

Add corresponding polygon IDs to cell metadata

Usage

addPolygonCells(
  gobject,
  polygon_name = "selections",
  spat_unit = "cell",
  spat_loc_name = "raw",
  feat_type = "rna",
  polygons = NULL,
  na.label = "no_polygon"
)

Arguments

gobject	A Giotto object
polygon_name	name of polygon selections
spat_unit	spatial unit
spat_loc_name	name of spatial locations to use
feat_type	feature name where metadata will be added
polygons	polygon names to plot (e.g. 'polygon_1'). If NULL, plots all available polygons
na.label	polygon label for cells located outside of polygons area. Default = "no_polygon"

Value

A Giotto object with a modified cell_metadata slot that includes the polygon name where each cell is located or no_polygon label if the cell is not located within a polygon area

Examples

## Not run: 
## Plot interactive polygons
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))

## Add polygon IDs to cell metadata
my_giotto_object <- addPolygonCells(my_giotto_object)

## End(Not run)

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