aggregate expression matrices from different z-stacks
Usage
aggregateStacks(
gobject,
spat_units,
feat_type,
values,
summarize_expression = "sum",
summarize_locations = "mean",
for_loop = FALSE,
for_loop_group_size = 100,
new_spat_unit = "aggregate",
verbose = TRUE
)Arguments
- gobject
giotto object
- spat_units
spatial units to aggregate
- feat_type
feature type
- values
values to use
- summarize_expression
method to summarize expression information
- summarize_locations
method to summarize spatial location information
- for_loop
aggregate polygons in for loop (default = FALSE)
- for_loop_group_size
size of polygon groups to aggregate in each loop
- new_spat_unit
new name for aggregated spatial unit
- verbose
verbosity
Details
Combines both aggregateStacksExpression
and aggregateStacksLocations
See also
Other aggregate stacks:
aggregateStacksExpression(),
aggregateStacksLocations(),
aggregateStacksPolygonOverlaps(),
aggregateStacksPolygons()
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"
aggregateStacks(g,
spat_units = c("z0", "z1"), feat_type = "rna",
values = "raw"
)
#> 1. Start aggregating expression data
#> > raw already exists and will be replaced with new values
#> > Cell metadata for spat_unit " aggregate " and feat_type " rna " already
#> exists and will be replaced with new metadata.
#> Setting cell metadata [aggregate][rna]
#> > Feat metadata for spat_unit " aggregate " and feat_type " rna " already
#> exists and will be replaced with new metadata.
#> Setting feature metadata [aggregate][rna]
#> 1. Aggregating expression data completed
#> 2. Start aggregating Polygon data
#> 2. Aggregating polygon data completed
#> 3. Start aggregating centroid location data
#> Start centroid calculation for polygon information
#> layer: aggregate
#> > spatial locations for polygon information layer " aggregate " and name " raw
#> " already exists and will be replaced
#> 3. Aggregating centroid location data completed
#> 4. Start aggregating polygon overlap data
#> 4. Aggregating polygon overlap data completed
#> 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