Get cells located within the polygons area
getCellsFromPolygon(
gobject,
polygon_name = "selections",
spat_unit = "cell",
spat_loc_name = "raw",
polygons = NULL
)
A Giotto object
name of polygon selections
spatial unit, default = 'cell'
name of spatial locations to use, default = 'raw'
character. A vector with polygon names to extract cells from. If NULL, cells from all polygons are retrieved
A terra 'SpatVector' with cell ID, x y coordinates, and polygon ID where each cell is located in.
## Plot interactive polygons
g <- GiottoData::loadGiottoMini("visium")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 3.1 read Giotto spatial shape information
#> cell_spatInfo_spatVector.shp
#> cell
#>
#> 3.2 read Giotto spatial centroid information
#> cell
#>
#> 3.3 read Giotto spatial overlap information
#> No overlaps were found, overlap loading will be
#> skipped
#>
#> 4. read Giotto image information
#> a giotto python environment was found
#> Using python path:
#> "/Users/yuanlab/Library/r-miniconda/envs/giotto_env/bin/pythonw"
my_polygon_coords <- data.frame(poly_ID = rep("polygon1", 3),
sdimx = c(5477, 5959, 4720), sdimy = c(-4125, -2808, -5202))
## Add polygon coordinates to Giotto object
my_giotto_polygons <- createGiottoPolygonsFromDfr(my_polygon_coords,
name = "selections")
#> Selecting col "poly_ID" as poly_ID column
#> Selecting cols "sdimx" and "sdimy" as x and y respectively
g <- addGiottoPolygons(
gobject = g,
gpolygons = list(my_giotto_polygons)
)
## Add polygon IDs to cell metadata
addPolygonCells(g)
#>
#> These column names were already used: in_tissue nr_feats perc_feats total_expr
#> leiden_clus custom_leiden
#> and will be overwritten
#> An object of class giotto
#> >Active spat_unit: cell
#> >Active feat_type: rna
#> [SUBCELLULAR INFO]
#> polygons : cell selections
#> [AGGREGATE INFO]
#> expression -----------------------
#> [cell][rna] raw normalized scaled
#> spatial locations ----------------
#> [cell] raw
#> spatial networks -----------------
#> [cell] Delaunay_network spatial_network
#> spatial enrichments --------------
#> [cell][rna] cluster_metagene DWLS
#> dim reduction --------------------
#> [cell][rna] pca custom_pca umap custom_umap tsne
#> nearest neighbor networks --------
#> [cell][rna] sNN.pca custom_NN
#> attached images ------------------
#> images : alignment image
#>
#>
#> Use objHistory() to see steps and params used
## Get only cells from polygon 1
getCellsFromPolygon(g)
#> class : SpatVector
#> geometry : points
#> dimensions : 17, 4 (geometries, attributes)
#> extent : 4720, 5959, -5202, -2808 (xmin, xmax, ymin, ymax)
#> coord. ref. :
#> names : sdimx sdimy cell_ID poly_ID
#> type : <int> <int> <chr> <chr>
#> values : 5477 -4125 AAAGGGATGTAGCAAG-1 polygon1
#> 5959 -2808 AAATGGCATGTCTTGT-1 polygon1
#> 4720 -5202 AAATGGTCAATGTGCC-1 polygon1