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Giotto schema

Source: R/methods-nesting.R
giotto_schema.Rd

Data within the giotto object is organized in a schema largely revolving around the spatial unit (which spatial length scale or polygonal annotation that is used as the unit of study) and the feature type (data modality). Information is then further organized based on the name or key of the object. In cases where a single spatial unit is comprised of information from multiple others, provenance is tracked to keep a record of which spatial units were the sources of that data. The functions to get and set these aspects of the schema on the Giotto object and subobjects are:

  • spatial unit: spatUnit(), spatUnit<-()

  • feature type: featType(), featType<-()

  • name: objName(), objName<-()

  • provenance: prov(), prov<-()

Usage

# S4 method for class 'ANY'
spatUnit(x)

# S4 method for class 'giotto'
spatUnit(x)

# S4 method for class 'list'
spatUnit(x)

# S4 method for class 'spatData'
spatUnit(x)

# S4 method for class 'giottoPolygon'
spatUnit(x)

# S4 method for class 'ANY'
spatUnit(x) <- value

# S4 method for class 'spatData'
spatUnit(x) <- value

# S4 method for class 'giottoPolygon'
spatUnit(x) <- value

# S4 method for class 'list'
spatUnit(x) <- value

# S4 method for class 'giotto'
spatUnit(x, old) <- value

# S4 method for class 'ANY'
featType(x)

# S4 method for class 'giotto'
featType(x)

# S4 method for class 'list'
featType(x)

# S4 method for class 'featData'
featType(x)

# S4 method for class 'ANY'
featType(x) <- value

# S4 method for class 'featData'
featType(x) <- value

# S4 method for class 'list'
featType(x) <- value

# S4 method for class 'giotto'
featType(x, old) <- value

# S4 method for class 'ANY'
objName(x)

# S4 method for class 'list'
objName(x)

# S4 method for class 'nameData'
objName(x)

# S4 method for class 'giottoPoints'
objName(x)

# S4 method for class 'giottoLargeImage'
objName(x)

# S4 method for class 'giottoImage'
objName(x)

# S4 method for class 'list'
objName(x) <- value

# S4 method for class 'nameData'
objName(x) <- value

# S4 method for class 'giottoImage'
objName(x) <- value

# S4 method for class 'giottoLargeImage'
objName(x) <- value

# S4 method for class 'giottoPoints'
objName(x) <- value

# S4 method for class 'provData'
prov(x)

# S4 method for class 'provData'
prov(x) <- value

Arguments

x

giotto or {Giotto} S4 subobject

value

value to set for this schema component

old

character. Old value to replace

Value

character. NA is returned when schema component is not applicable to target object. If using the replacement function, the giotto object or subobject is returned

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

########### Get/set existing schema values within giotto object ####
spatUnit(g)
#> [1] "aggregate" "z0"        "z1"       
featType(g)
#> [1] "rna"

# rename a spatial unit
spatUnit(g, old = "z0") <- "slice1"
#> Warning: activeSpatUnit 'z0' no longer exists.
#>  activeSpatUnit defaulted to 'aggregate'
spatUnit(g)
#> [1] "aggregate" "slice1"    "z1"       

# rename a feature type
featType(g, old = "rna") <- "feature1"
#> Warning: activeFeatType 'rna' no longer exists.
#>  activeFeatType defaulted to 'feature1'
featType(g)
#> [1] "feature1"

########### Get schema values from a list of objects ###############

glist <- as.list(g)
spatUnit(glist)
#>  [1] "slice1"    "z1"        "aggregate" "slice1"    "z1"        "aggregate"
#>  [7] "aggregate" "aggregate" NA          "slice1"    "z1"        "aggregate"
#> [13] "aggregate" "aggregate" "aggregate" "slice1"    "z1"        "aggregate"
#> [19] "slice1"    "z1"        "aggregate" "aggregate" "aggregate" "aggregate"
#> [25] "aggregate" "aggregate" NA          NA          NA          NA         
featType(glist)
#>  [1] NA         NA         NA         NA         NA         NA        
#>  [7] NA         NA         "feature1" "feature1" "feature1" "feature1"
#> [13] "feature1" "feature1" "feature1" "feature1" "feature1" "feature1"
#> [19] "feature1" "feature1" "feature1" "feature1" "feature1" "feature1"
#> [25] "feature1" "feature1" NA         NA         NA         NA        
objName(glist)
#>  [1] "slice1"           "z1"               "aggregate"        "raw"             
#>  [5] "raw"              "raw"              "Delaunay_network" "kNN_network"     
#>  [9] "feature1"         "raw"              "raw"              "raw"             
#> [13] "normalized"       "scaled"           "pearson"          NA                
#> [17] NA                 NA                 NA                 NA                
#> [21] NA                 "cluster_metagene" "sNN.pca"          "pca"             
#> [25] "umap"             "tsne"             "dapi_z0"          "dapi_z1"         
#> [29] "polyT_z0"         "polyT_z1"        

########### Get and set schema values with single subobject ########

fx <- g[["feat_meta", spat_unit = "aggregate"]][[1]]

spatUnit(fx)
#> [1] "aggregate"
spatUnit(fx) <- "foo"
spatUnit(fx)
#> [1] "foo"

featType(fx)
#> [1] "feature1"
featType(fx) <- "bar"
featType(fx)
#> [1] "bar"

ex <- g[["expression", spat_unit = "aggregate"]][[1]]

objName(ex)
#> [1] "raw"
objName(ex) <- "baz"
objName(ex)
#> [1] "baz"

prov(ex)
#> [1] "z0" "z1"
prov(ex) <- "qux"
prov(ex)
#> [1] "qux"