Set polygon information into Giotto object
Usage
setPolygonInfo(
gobject,
x,
name = "cell",
centroids_to_spatlocs = FALSE,
verbose = TRUE,
initialize = TRUE,
...
)Arguments
- gobject
giotto object
- x
single object or named list of objects to set as polygon information (see details)
- name
(optional, character) name to assign to polygon and spatial unit that polygon might define. Only used for single giottoPolygon objects. Names are taken from a named list for multiple polygons.
- centroids_to_spatlocs
if centroid information is discovered, whether to additionally set them as a set of spatial locations (default = FALSE)
- verbose
be verbose
- initialize
(default = FALSE) whether to initialize the gobject before returning
- ...
additional params to pass
Details
Inputs can be provided as either single objects or named lists of
objects. If the list is not named, then a generic name of the template
'cell_i' will be applied.
If an input is a character string, then it is assumed that it is a
filepath.
For required formatting when reading tabular data or objects, see
createGiottoPolygonsFromDfr details.
See also
Other polygon info data accessor functions:
getPolygonInfo()
Other functions to set data in giotto object:
setCellMetadata(),
setDimReduction(),
setExpression(),
setFeatureInfo(),
setFeatureMetadata(),
setGiotto(),
setGiottoImage(),
setMultiomics(),
setNearestNetwork(),
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"
polyinfo <- getPolygonInfo(g, return_giottoPolygon = TRUE)
setPolygonInfo(gobject = g, x = polyinfo)
#> > " z0 " already exists and will be replaced
#> with new giotto polygon
#> Setting polygon info [z0]
#> 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