Function to get expression values from giotto object
Usage
getExpression(
gobject,
values = NULL,
spat_unit = NULL,
feat_type = NULL,
output = c("exprObj", "matrix"),
set_defaults = TRUE
)Arguments
- gobject
giotto object
- values
expression values to extract (e.g. "raw", "normalized", "scaled")
- spat_unit
spatial unit (e.g. "cell")
- feat_type
feature type (e.g. "rna", "dna", "protein")
- output
what object type to retrieve the expression as. Currently either matrix' for the matrix object contained in the exprObj or 'exprObj' (default) for the exprObj itself are allowed.
- 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 expression accessor functions:
setExpression()
Other functions to get data from giotto object:
getCellMetadata(),
getDimReduction(),
getFeatureInfo(),
getFeatureMetadata(),
getGiottoImage(),
getMultiomics(),
getNearestNetwork(),
getPolygonInfo(),
getSpatialEnrichment(),
getSpatialGrid(),
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
getExpression(g)
#> Error in UseMethod("getExpression"): no applicable method for 'getExpression' applied to an object of class "giotto"