Compare cell types percent per polygon
compareCellAbundance(
gobject,
polygon_name = "selections",
spat_unit = "cell",
feat_type = "rna",
cell_type_column = "leiden_clus",
...
)
A Giotto object
name of polygon selections
spatial unit. Default = "cell"
feature type. Default = "rna"
column name within the cell metadata table to use
Additional parameters passed to ComplexHeatmap::Heatmap
A ComplexHeatmap::Heatmap
## 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 cells
g <- addPolygonCells(g)
#>
#> These column names were already used: in_tissue nr_feats perc_feats total_expr
#> leiden_clus custom_leiden
#> and will be overwritten
compareCellAbundance(g)