Get giotto points spatVector
Usage
getFeatureInfo(
gobject = gobject,
feat_type = NULL,
return_giottoPoints = FALSE,
set_defaults = TRUE,
simplify = TRUE
)Arguments
- gobject
giotto object
- feat_type
feature type (e.g. "rna", "dna", "protein")
- return_giottoPoints
return as a giottoPoints object
- set_defaults
set default spat_unit and feat_type. Change to FALSE only when expression and spat_info are not expected to exist.
- simplify
logical. Whether or not to take object out of a list when there is a length of 1.
See also
Other feature info data accessor functions:
setFeatureInfo()
Other functions to get data from giotto object:
getCellMetadata(),
getDimReduction(),
getExpression(),
getFeatureMetadata(),
getGiottoImage(),
getMultiomics(),
getNearestNetwork(),
getPolygonInfo(),
getSpatialEnrichment(),
getSpatialGrid(),
getSpatialLocations(),
getSpatialNetwork(),
get_multiomics()
Examples
g <- GiottoData::loadGiottoMini("vizgen")
#> 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"
getFeatureInfo(g)
#> class : SpatVector
#> geometry : points
#> dimensions : 79761, 3 (geometries, attributes)
#> extent : 6400.037, 6900.032, -5149.983, -4699.979 (xmin, xmax, ymin, ymax)
#> source : rna_feature_spatVector.shp
#> coord. ref. :
#> names : feat_ID global_z feat_ID_uniq
#> type : <chr> <num> <num>
#> values : Mlc1 0 1
#> Gprc5b 0 2
#> Gfap 0 3