Function to set feature metadata into giotto object
Usage
setFeatureMetadata(
gobject,
x,
spat_unit = NULL,
feat_type = NULL,
provenance = NULL,
verbose = TRUE,
initialize = TRUE,
...
)Arguments
- gobject
giotto object
- x
featMetaObj or list of featMetaObj to set. Passing NULL will reset a specified set of feature metadata in the giotto object.
- spat_unit
spatial unit (e.g. "cell")
- feat_type
feature type (e.g. "rna", "dna", "protein")
- provenance
provenance information (optional)
- verbose
be verbose
- initialize
(default = FALSE) whether to initialize the gobject before returning
- ...
additional params to pass
See also
Other functions to set data in giotto object:
setCellMetadata(),
setDimReduction(),
setExpression(),
setFeatureInfo(),
setGiotto(),
setGiottoImage(),
setMultiomics(),
setNearestNetwork(),
setPolygonInfo(),
setSpatialEnrichment(),
setSpatialGrid(),
setSpatialLocations(),
setSpatialNetwork(),
set_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"
m1 <- getFeatureMetadata(g, output = "data.table")
m2 <- data.frame(
feat_ID = m1$feat_ID,
new_column = paste0("gene_", m1$feat_ID)
)
setFeatureMetadata(gobject = g, x = createFeatMetaObj(m2))
#> Setting feature metadata [cell][rna]
#> An object of class giotto
#> >Active spat_unit: z0
#> >Active feat_type: rna
#> dimensions : 337, 498 (features, cells)
#> [SUBCELLULAR INFO]
#> polygons : z0 z1 aggregate
#> features : rna
#> [AGGREGATE INFO]
#> expression -----------------------
#> [z0][rna] raw
#> [z1][rna] raw
#> [aggregate][rna] raw normalized scaled pearson
#> spatial locations ----------------
#> [z0] raw
#> [z1] raw
#> [aggregate] raw
#> spatial networks -----------------
#> [aggregate] Delaunay_network kNN_network
#> spatial enrichments --------------
#> [aggregate][rna] cluster_metagene
#> dim reduction --------------------
#> [aggregate][rna] pca umap tsne
#> nearest neighbor networks --------
#> [aggregate][rna] sNN.pca
#> attached images ------------------
#> images : 4 items...
#>
#>
#> Use objHistory() to see steps and params used