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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

Value

giotto object

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