Function to get spatial grid
Usage
getSpatialGrid(
gobject,
spat_unit = NULL,
feat_type = NULL,
name = NULL,
return_grid_Obj = FALSE,
set_defaults = TRUE
)Arguments
- gobject
giotto object
- spat_unit
spatial unit (e.g. "cell")
- feat_type
feature type (e.g. "rna", "dna", "protein")
- name
name of spatial grid
- return_grid_Obj
return grid object (default = FALSE)
- set_defaults
set default spat_unit and feat_type. Change to FALSE only when expression and spat_info are not expected to exist.
See also
Other spatial grid data accessor functions:
setSpatialGrid()
Other functions to get data from giotto object:
getCellMetadata(),
getDimReduction(),
getExpression(),
getFeatureInfo(),
getFeatureMetadata(),
getGiottoImage(),
getMultiomics(),
getNearestNetwork(),
getPolygonInfo(),
getSpatialEnrichment(),
getSpatialLocations(),
getSpatialNetwork(),
get_multiomics()
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)
getSpatialGrid(g)
#> The grid name was not specified, default to the first: "spatial_grid"
#> x_start y_start x_end y_end gr_name gr_x_name gr_y_name
#> <num> <num> <num> <num> <char> <char> <char>
#> 1: 3067.5 -5445 3072.5 -5440 gr_1 gr_x_1 gr_y_1
#> 2: 3072.5 -5445 3077.5 -5440 gr_2 gr_x_2 gr_y_1
#> 3: 3077.5 -5445 3082.5 -5440 gr_3 gr_x_3 gr_y_1
#> 4: 3082.5 -5445 3087.5 -5440 gr_4 gr_x_4 gr_y_1
#> 5: 3087.5 -5445 3092.5 -5440 gr_5 gr_x_5 gr_y_1
#> ---
#> 388796: 6417.5 -2570 6422.5 -2565 gr_388796 gr_x_671 gr_y_576
#> 388797: 6422.5 -2570 6427.5 -2565 gr_388797 gr_x_672 gr_y_576
#> 388798: 6427.5 -2570 6432.5 -2565 gr_388798 gr_x_673 gr_y_576
#> 388799: 6432.5 -2570 6437.5 -2565 gr_388799 gr_x_674 gr_y_576
#> 388800: 6437.5 -2570 6442.5 -2565 gr_388800 gr_x_675 gr_y_576