Function to set expression values for giotto object.
Usage
setExpression(
gobject,
x,
spat_unit = NULL,
feat_type = NULL,
name = "raw",
provenance = NULL,
verbose = TRUE,
initialize = TRUE,
...
)Arguments
- gobject
giotto object
- x
exprObj or list of exprObj to set. Passing NULL will remove a specified set of expression data from the giotto object
- spat_unit
spatial unit (e.g. "cell")
- feat_type
feature type (e.g. "rna", "dna", "protein")
- name
name for the expression information
- provenance
provenance information (optional) information for the giotto object. Pass NULL to remove an expression object
- verbose
be verbose
- initialize
(default = FALSE) whether to initialize the gobject before returning
- ...
additional params to pass
See also
Other expression accessor functions:
getExpression()
Other functions to set data in giotto object:
setCellMetadata(),
setDimReduction(),
setFeatureInfo(),
setFeatureMetadata(),
setGiotto(),
setGiottoImage(),
setMultiomics(),
setNearestNetwork(),
setPolygonInfo(),
setSpatialEnrichment(),
setSpatialGrid(),
setSpatialLocations(),
setSpatialNetwork(),
set_multiomics()
Examples
g <- createGiottoObject()
#> 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"
m <- matrix(rnorm(100), nrow = 10)
colnames(m) <- paste0("cell_", seq_len(10))
rownames(m) <- paste0("feat_", seq_len(10))
g <- setExpression(gobject = g, x = createExprObj(m, name = "raw"))
#> Setting expression [cell][rna] raw