Giotto object spatial values — spatValues • GiottoClass

Retrieve specific values from the giotto object for a specific spat_unit and feat_type. Values are returned as a data.table with the features requested and a cell_ID column. This function may be updated in the future to search in additional sets of information. To see the currently available slot it checks, see details.

Usage

spatValues(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  feats,
  expression_values = NULL,
  spat_enr_name = NULL,
  poly_info = NULL,
  verbose = NULL,
  debug = FALSE
)

Arguments

gobject: giotto object
spat_unit: character. spatial unit to check
feat_type: character. feature type to check
feats: character vector. One or more features or values to find within the giotto object
expression_values: character. (optional) Name of expression information to use
spat_enr_name: character. (optional) Name of spatial enrichments to use
poly_info: character. (optional) Name of polygons to use
verbose: verbosity
debug: logical. (default = FALSE) See details.

Value

A data.table with a cell_ID column and whichever feats were requested

Details

[search]
spatValues searches through the set of available information within the giotto object for matches to feats. The current search order is

cell expression
cell metadata
spatial enrichment
polygon info

If a specific name for one of the types of information is provided via a param such as expression_values, spat_enr_name, poly_info, then the search will only be performed on that type of data.

[debug]
This function uses Giotto's accessor functions which can usually throw errors whenever a specific set of data or the features within that set do not exist. This function muffles those errors, and only sends an error that the data was not found when all getters fail. By setting debug = TRUE, you can see the errors returned from each failed getter printed as messages for easier debugging.

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"

# expression
spatValues(g, spat_unit = "aggregate", feats = c("Mlc1", "Gfap"))
#> Getting values from [aggregate][rna][raw] expression
#>                                      cell_ID  Mlc1  Gfap
#>                                       <char> <num> <num>
#>   1: 240649020551054330404932383065726870513     0     2
#>   2: 274176126496863898679934791272921588227     0     0
#>   3: 323754550002953984063006506310071917306     0     2
#>   4:  87260224659312905497866017323180367450     0     1
#>   5:  17817477728742691260808256980746537959     0     0
#>  ---                                                    
#> 458:   6380671372744430258754116433861320161     2     2
#> 459:  75286702783716447443887872812098770697     1     2
#> 460:   9677424102111816817518421117250891895     3     1
#> 461:  17685062374745280598492217386845129350     0     3
#> 462:  32422253415776258079819139802733069941     0     4
spatValues(g,
    spat_unit = "aggregate", feats = c("Mlc1", "Gfap"),
    expression_values = "normalized"
)
#> Getting values from [aggregate][rna][normalized] expression
#>                                      cell_ID     Mlc1      Gfap
#>                                       <char>    <num>     <num>
#>   1: 240649020551054330404932383065726870513 0.000000 10.481367
#>   2: 274176126496863898679934791272921588227 0.000000  0.000000
#>   3: 323754550002953984063006506310071917306 0.000000  7.901442
#>   4:  87260224659312905497866017323180367450 0.000000  5.886051
#>   5:  17817477728742691260808256980746537959 0.000000  0.000000
#>  ---                                                           
#> 458:   6380671372744430258754116433861320161 6.701726  6.701726
#> 459:  75286702783716447443887872812098770697 5.644422  6.629928
#> 460:   9677424102111816817518421117250891895 7.878817  6.306062
#> 461:  17685062374745280598492217386845129350 0.000000 11.065993
#> 462:  32422253415776258079819139802733069941 0.000000 10.041155

# spatial enrichment
spatValues(g, spat_unit = "aggregate", feats = c("1", "3"))
#> Getting values from [aggregate][rna][cluster_metagene] spatial enrichment
#>                                      cell_ID         1         3
#>                                       <char>     <num>     <num>
#>   1: 240649020551054330404932383065726870513 1.0148370 0.3160792
#>   2: 274176126496863898679934791272921588227 3.2074150 0.6728505
#>   3: 323754550002953984063006506310071917306 3.9536614 0.0000000
#>   4:  87260224659312905497866017323180367450 4.0936217 0.1962017
#>   5:  17817477728742691260808256980746537959 0.9789911 1.9563931
#>  ---                                                            
#> 458:   6380671372744430258754116433861320161 2.2465293 0.1905173
#> 459:  75286702783716447443887872812098770697 1.3827322 0.0000000
#> 460:   9677424102111816817518421117250891895 3.6843575 0.0000000
#> 461:  17685062374745280598492217386845129350 1.0010248 0.0000000
#> 462:  32422253415776258079819139802733069941 2.3449006 0.0000000

# polygon info
spatValues(g, spat_unit = "aggregate", feats = c("agg_n", "valid"))
#> Getting values from [aggregate] polygon info
#>                                      cell_ID agg_n valid
#>                                       <char> <int> <int>
#>   1: 100210519278873141813371229408401071444     2     1
#>   2: 101161259912191124732236989250178928032     2     1
#>   3: 101488859781016188084173008420811094152     2     1
#>   4: 101523780333017320796881555775415156847     2     1
#>   5: 102184699197574201819246996094734116255     2     1
#>  ---                                                    
#> 458:   9677424102111816817518421117250891895     2     1
#> 459:  97068595823890802071024838798130036179     2     1
#> 460:  97411078642927912684859796714759494710     2     1
#> 461:   9816437869021910185567097363182418837     2     1
#> 462:  98561957902191275233320065611022298397     2     1

# cell meta
spatValues(g, spat_unit = "aggregate", feats = c("nr_feats"))
#> Getting values from [aggregate][rna] cell metadata
#>                                      cell_ID nr_feats
#>                                       <char>    <int>
#>   1: 240649020551054330404932383065726870513        5
#>   2: 274176126496863898679934791272921588227       27
#>   3: 323754550002953984063006506310071917306       23
#>   4:  87260224659312905497866017323180367450       37
#>   5:  17817477728742691260808256980746537959       18
#>  ---                                                 
#> 458:   6380671372744430258754116433861320161       54
#> 459:  75286702783716447443887872812098770697       45
#> 460:   9677424102111816817518421117250891895       30
#> 461:  17685062374745280598492217386845129350        5
#> 462:  32422253415776258079819139802733069941       12