annotate_spatlocs_with_spatgrid_3D
Source:R/spatial_structures.R
annotate_spatlocs_with_spatgrid_3D.Rdannotate spatial locations with 3D spatial grid information
Examples
g <- GiottoData::loadGiottoMini("starmap")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial 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_spatloc <- getSpatialLocations(g, output = "data.table")
g_spatgrid <- getSpatialGrid(g)
#> The grid name was not specified, default to the first: "spatial_grid"
annotate_spatlocs_with_spatgrid_3D(
spatloc = g_spatloc,
spatgrid = g_spatgrid
)
#> sdimx sdimy sdimz cell_ID gr_x_loc gr_y_loc gr_z_loc gr_loc
#> <int> <int> <int> <char> <char> <char> <char> <char>
#> 1: 270 212 19 cell_2944 gr_x_2 gr_y_2 gr_z_2 gr_83
#> 2: 1389 1215 54 cell_17523 gr_x_7 gr_y_7 gr_z_4 gr_277
#> 3: 1051 360 89 cell_30080 gr_x_6 gr_y_2 gr_z_5 gr_303
#> 4: 592 777 10 cell_941 gr_x_3 gr_y_5 gr_z_1 gr_39
#> 5: 1058 223 84 cell_28514 gr_x_6 gr_y_2 gr_z_5 gr_303
#> ---
#> 3901: 348 1383 78 cell_26011 gr_x_2 gr_y_8 gr_z_5 gr_353
#> 3902: 674 1080 89 cell_31539 gr_x_4 gr_y_6 gr_z_5 gr_337
#> 3903: 919 532 22 cell_4185 gr_x_5 gr_y_3 gr_z_2 gr_95
#> 3904: 947 885 23 cell_3851 gr_x_5 gr_y_5 gr_z_2 gr_113
#> 3905: 144 439 60 cell_21337 gr_x_1 gr_y_3 gr_z_4 gr_235