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_loc_name = NULL,
spat_enr_name = NULL,
poly_info = NULL,
dim_reduction_to_use = NULL,
dim_reduction_name = NULL,
verbose = NULL,
debug = FALSE
)Arguments
- gobject
giottoobject- 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_loc_name
character. (optional) Name of spatial locations information to use
- spat_enr_name
character. (optional) Name of spatial enrichments to use
- poly_info
character. (optional) Name of polygons to use
- dim_reduction_to_use
character. (optional) Which type of dimension reduction to use
- dim_reduction_name
character. (optional) Name of dimension reduction to use
- verbose
verbosity
- debug
logical. (default = FALSE) See details.
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 locations
spatial enrichment
dimension reduction
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, etc, 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> <num> <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