Get the cell IDs (termed spatial IDs to better reflect when not at the single-cell level) and feature IDs of a giotto object or subobject.
[giotto object specific]
When applied on a giotto object, these functions pull from the cell_ID
and feat_ID slots. The values within these slots are updated whenever the
object is data is changed and, importantly, whenever the active spat_unit and
feat_type is set (see activeSpatUnit() and activeFeatType()). New values
for these slots are specific to the active spat_unit and feat_type and are
detected from either the subcellular
level (giottoPolygon and giottoPoints) or the aggregate
level (expression matrix) data, with a preference for the latter if it
exists. Be aware that with this current behavior, values returned
byspatIDs() and featIDs() should be regarded as the minimal set of
expected IDs within all giotto slots, and not always the exact set or
ordering.
Usage
# S4 method for class 'giotto'
spatIDs(x, spat_unit = NULL, subset, negate = FALSE, quote = TRUE, ...)
# S4 method for class 'exprObj'
spatIDs(x, ...)
# S4 method for class 'spatLocsObj'
spatIDs(x, ...)
# S4 method for class 'cellMetaObj'
spatIDs(x, ...)
# S4 method for class 'spatialNetworkObj'
spatIDs(x, ...)
# S4 method for class 'dimObj'
spatIDs(x, ...)
# S4 method for class 'giottoPolygon'
spatIDs(x, use_cache = TRUE, uniques = TRUE, ...)
# S4 method for class 'spatEnrObj'
spatIDs(x, ...)
# S4 method for class 'nnNetObj'
spatIDs(x, ...)
# S4 method for class 'giotto'
featIDs(x, feat_type = NULL, subset, negate = FALSE, quote = TRUE, ...)
# S4 method for class 'exprObj'
featIDs(x, ...)
# S4 method for class 'featMetaObj'
featIDs(x, ...)
# S4 method for class 'giottoPoints'
featIDs(x, use_cache = TRUE, uniques = TRUE, ...)
# S4 method for class 'spatEnrObj'
featIDs(x, ...)Arguments
- x
an object
- spat_unit
(optional) specify which spatial unit
- subset
logical expression to find a subset of features.
- negate
logical. if
TRUEall IDs that are not in thesubsetare selected- quote
logical. If
TRUE, thesubsetparam will be quoted withsubstitute(). Set this toFALSEwhen calling from a function, although that may not be recommended since NSE output can be unexpected when not used interactively.- ...
additional params to pass when used with the
subsetparam. ForspatID(), these pass tospatValues(). ForfeatID(), these currently only pass tofDataDT().- use_cache
use cached IDs if available (gpoly and gpoints only)
- uniques
return unique ID values only (currently gpoly and gpoints only)
- feat_type
(optional) specify which feature type
Examples
g <- GiottoData::loadGiottoMini("vis")
#> Error in match.arg(dataset, choices = c(names(mini_gobject_manifest))): 'arg' should be one of “visium”, “visium_multisample”, “vizgen”, “cosmx”, “seqfish”, “starmap”, “spatialgenomics”
spatIDs(g)
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'spatIDs': object 'g' not found
spatIDs(g, subset = nr_feats <= 200)
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'spatIDs': object 'g' not found
spatIDs(g, subset = Dim.1 > 25, dim_reduction_to_use = "umap")
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'spatIDs': object 'g' not found
featIDs(g)
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'featIDs': object 'g' not found
featIDs(g, subset = nr_cells < 100)
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'featIDs': object 'g' not found
gpoints <- GiottoData::loadSubObjectMini("giottoPoints")
featIDs(gpoints)
#> [1] "Mlc1" "Gprc5b" "Gfap" "Ednrb" "Sox9" "Aqp4"
#> [7] "Gjc3" "Sox8" "Ntsr2" "Adcyap1r1" "Smo" "Gpr161"
#> [13] "C1qb" "Olig1" "C1qa" "Lmtk2" "Pth1r" "Ephb6"
#> [19] "Gpr26" "Gabbr1" "Adra2a" "Gabbr2" "Timp4" "Abcc9"
#> [25] "Csf1r" "Ntrk2" "Adgrg1" "Ntrk3" "Ddr1" "Erbb4"
#> [31] "Selplg" "Cspg5" "Dlk1" "Gpr37l1" "Fzd1" "Fgfr3"
#> [37] "Slc25a18" "Igf1r" "Adgrl1" "S1pr1" "Ryk" "Grm5"
#> [43] "Eomes" "Axl" "Efemp1" "Adgrb3" "Sstr4" "Fn1"
#> [49] "Adora1" "Erbb2" "Gper1" "Gramd3" "Mertk" "Slc32a1"
#> [55] "Adgra1" "Adgrl2" "Ptgfr" "Fzd2" "Aldh1l1" "Adgrg6"
#> [61] "Egfr" "Gpr162" "Lpar4" "Kit" "Ptgdr" "Gad1"
#> [67] "Lgr4" "Tyro3" "Atp13a5" "Ddr2" "Rspo3" "Arhgap29"
#> [73] "Ackr3" "Gpr146" "Fzd7" "Slc47a1" "Insr" "Ptger3"
#> [79] "Bdkrb1" "Traf4" "Celsr2" "Fzd4" "Fgfr2" "Cx3cr1"
#> [85] "Anxa11" "Adgrb1" "Lpar1" "Gpr17" "Gpr173" "Ror1"
#> [91] "Cxcl12" "Kiss1r" "Epha4" "Gpr182" "Man1a" "Gpr4"
#> [97] "P2ry14" "Hcar1" "Ephb1" "Adrb1" "Grm3" "P2ry1"
#> [103] "Nrp2" "Ptk7" "Slco1a4" "Tmem108" "Hrh3" "Insrr"
#> [109] "Cmklr1" "Opn3" "Adra1b" "Gpr62" "Npy1r" "Nrp1"
#> [115] "Fzd6" "S1pr5" "Pdgfrb" "Flt1" "Chrm3" "Agtr1a"
#> [121] "Adgrl4" "Ephb3" "Lpar6" "Epha6" "Fzd5" "Emcn"
#> [127] "Cldn5" "Sstr1" "Fzd3" "P2ry12" "Adgrl3" "Sema4d"
#> [133] "Adgrf5" "Gpr160" "Mrgpre" "Amigo2" "Adgra3" "P2yr13"
#> [139] "Epha3" "Adgre1" "P2ry6" "Cx3cl1" "Epha10" "Tacr1"
#> [145] "Peg10" "Ednra" "Plxnb3" "Flt4" "Slc17a7" "Drd2"
#> [151] "Tjap1" "Fzd8" "Cd300c2" "Htr4" "Gpr52" "Tek"
#> [157] "S1pr2" "Kdr" "Ror2" "Kcnj8" "Hrh1" "Celsr1"
#> [163] "Gpr153" "S1pr3" "Adgra2" "Fgfrl1" "Tie1" "Slc15a3"
#> [169] "Ccr10" "Pdgfra" "Lhcgr" "Mrgprf" "Ascl1" "Baiap2"
#> [175] "Gpr85" "Gpr22" "Gcgr" "Grm1" "Ptafr" "Calcrl"
#> [181] "Gpr34" "Cenpe" "Adora2b" "Adrb2" "Ccr2" "Alk"
#> [187] "Tacr3" "Chrm5" "Erbb3" "Ccr9" "Gpr21" "Epha7"
#> [193] "Adra2b" "Pcdh15" "Blank-104" "Adora2a" "Drd1" "Blank-57"
#> [199] "Grm7" "Htr1b" "Fzd9" "Grm4" "Blank-152" "Aplnr"
#> [205] "Gpr176" "F2r" "Vmn1r43" "Gpr156" "Gpr55" "Blank-155"
#> [211] "Bdkrb2" "C5ar2" "Gpbar1" "Adgrv1" "Gprc5c" "Lmod1"
#> [217] "Gpr135" "Rxfp3" "Tbxa2r" "Fzd10" "Ret" "Blank-80"
#> [223] "Epha8" "Gpr75" "Ackr1" "Adgrg4" "Chrm1" "Epha1"
#> [229] "Vmn2r1" "Syt4" "Tas2r135" "Ccr1" "Lpar2" "Myh11"
#> [235] "Gipr" "Musk" "Gpr183" "Cnr1" "C3ar1" "S1pr4"
#> [241] "Grm2" "C5ar1" "Ephb2" "Fpr1" "Rho" "Gpr27"
#> [247] "Adra1d" "Gpr157" "Adgrg2" "Blank-45" "Gpr20" "Casr"
#> [253] "Avpr2" "Mc5r" "Sctr" "Epha5" "Gpr158" "Cxcr4"
#> [259] "Vipr1" "Gpr6" "Blank-148" "Celsr3" "Uts2r" "Hrh2"
#> [265] "Htr6" "Slc17a6" "Gpr1" "Glp2r" "Ppp1r3g" "V1ra8"
#> [271] "Trhr" "Sstr3" "Gpr63" "Htr1a" "F2rl3" "Pln"
#> [277] "Grin2b" "Gpr37" "Chrm4" "Lgr6" "Gpr61" "Taar7e"
#> [283] "Mas1" "Npy2r" "Ptger2" "P2ry2" "Oprm1" "Prokr2"
#> [289] "Adra1a" "Gpr45" "Mc4r" "Blank-128" "Sstr2" "Flt3"
#> [295] "Htr5a" "Ghsr" "Galr1" "Blank-95" "Gpr83" "Crhr1"
#> [301] "Brs3" "Drd5" "Gpr139" "Taar6" "Htr5b" "Vmn1r40"
#> [307] "Rrh" "Blank-83" "Crhr2" "Blank-161" "Vmn1r50" "Tas1r3"
#> [313] "Taar2" "P2ry4" "Mchr1" "Tas1r1" "Blank-69" "Htr7"
#> [319] "Hcrtr2" "Htr2a" "Cysltr2" "Vmn1r46" "Grpr" "Adgrf2"
#> [325] "Blank-127" "Opn5" "Taar3" "Oxtr" "Cckbr" "Nmbr"
#> [331] "Ptger4" "Blank-145" "Gpr101" "Slc17a8" "Adgrf4" "Epha2"
#> [337] "Blank-139"