annotate spatial grid with cell ID and cell metadata (optional)
Usage
annotateSpatialGrid(
gobject,
spat_unit = NULL,
feat_type = NULL,
spat_loc_name = "raw",
spatial_grid_name = "spatial_grid",
cluster_columns = NULL
)Arguments
- gobject
Giotto object
- spat_unit
spatial unit
- feat_type
feature type
- spat_loc_name
name of spatial locations
- spatial_grid_name
name of spatial grid, see
showGiottoSpatGrids- cluster_columns
names of cell metadata, see
pDataDT
Examples
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
#> 3.2 read Giotto spatial centroid information
#> 3.3 read Giotto spatial overlap information
#> 4. read Giotto image information
#> python already initialized in this session
#> active environment : 'giotto_env'
#> python version : 3.10
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#> "/usr/share/miniconda/envs/giotto_env/bin/python"
g <- createSpatialGrid(g, sdimx_stepsize = 5, sdimy_stepsize = 5)
annotateSpatialGrid(g)
#> sdimx sdimy cell_ID gr_x_loc gr_y_loc gr_loc
#> <int> <int> <char> <char> <char> <char>
#> 1: 5477 -4125 AAAGGGATGTAGCAAG-1 gr_x_482 gr_y_264 gr_178007
#> 2: 5959 -2808 AAATGGCATGTCTTGT-1 gr_x_579 gr_y_528 gr_356304
#> 3: 4720 -5202 AAATGGTCAATGTGCC-1 gr_x_331 gr_y_49 gr_32731
#> 4: 5202 -5322 AAATTAACGGGTAGCT-1 gr_x_427 gr_y_25 gr_16627
#> 5: 4101 -4604 AACAACTGGTAGTTGC-1 gr_x_207 gr_y_169 gr_113607
#> ---
#> 620: 4996 -5442 TTGTAATCCGTACTCG-1 gr_x_386 gr_y_1 gr_386
#> 621: 6303 -2688 TTGTATCACACAGAAT-1 gr_x_648 gr_y_552 gr_372573
#> 622: 5202 -3885 TTGTCGTTCAGTTACC-1 gr_x_427 gr_y_312 gr_210352
#> 623: 5340 -3406 TTGTGGCCCTGACAGT-1 gr_x_455 gr_y_408 gr_275180
#> 624: 5615 -4125 TTGTTCAGTGTGCTAC-1 gr_x_510 gr_y_264 gr_178035