Prints the available spatial grids that are attached to the Giotto object
See also
Other functions to show data in giotto object:
showGiottoCellMetadata(),
showGiottoDimRed(),
showGiottoExpression(),
showGiottoFeatInfo(),
showGiottoFeatMetadata(),
showGiottoImageNames(),
showGiottoNearestNetworks(),
showGiottoSpatEnrichments(),
showGiottoSpatLocs(),
showGiottoSpatNetworks(),
showGiottoSpatialInfo()
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)
showGiottoSpatGrids(g)
#> └──Spatial unit "cell"
#> └──Feature type "rna"
#> └──S4 spatialGridObj "spatial_grid" (388800 rows)
#> 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
#>