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")
#> 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"
spatIDs(g)
#> [1] "AAAGGGATGTAGCAAG-1" "AAATGGCATGTCTTGT-1" "AAATGGTCAATGTGCC-1"
#> [4] "AAATTAACGGGTAGCT-1" "AACAACTGGTAGTTGC-1" "AACAGGAAATCGAATA-1"
#> [7] "AACAGGATGGGCCGCG-1" "AACCATGGGATCGCTA-1" "AACCCAGAGACGGAGA-1"
#> [10] "AACCGAGCTTGGTCAT-1" "AACCGTTGTGTTTGCT-1" "AACGATAGAAGGGCCG-1"
#> [13] "AACGATATGTCAACTG-1" "AACGCGGTCTCCAGCC-1" "AACGTCAGACTAGTGG-1"
#> [16] "AACTCGATGGCGCAGT-1" "AACTGATATTAGGCCT-1" "AACTGGGTCCCGACGT-1"
#> [19] "AACTTGCCCGTATGCA-1" "AAGAGATGAATCGGTA-1" "AAGCTCGTGCCAAGTC-1"
#> [22] "AAGGAGCGGTTGGTGC-1" "AAGGCGCGTAAAGCTT-1" "AAGGCTGTGCTCATCG-1"
#> [25] "AAGTAGAAGACCGGGT-1" "AAGTAGTGACGCGAGG-1" "AATCCAAGGGCCTGAG-1"
#> [28] "AATGACTGTCAGCCGG-1" "AATGCAACCGGGTACC-1" "AATGGTTCTCACAAGC-1"
#> [31] "AATTTGGTTCCAAAGA-1" "ACAACAGCATGAGCTA-1" "ACAACGGTCCCTGCGA-1"
#> [34] "ACAAGGACAAGAGGTT-1" "ACACAAAGACGGGTGG-1" "ACACACTTTCTACACG-1"
#> [37] "ACACCCAGCATGCAGC-1" "ACACCCGAGAAATCCG-1" "ACACCTTAAGTAGGGC-1"
#> [40] "ACACGAGACTCCTTCT-1" "ACACGGGAACTTAGGG-1" "ACATAATAAGGCGGTG-1"
#> [43] "ACCAAGAACGCGTGTC-1" "ACCACAAGTTTCTATC-1" "ACCCTTCATCTGCGAA-1"
#> [46] "ACCGACTGAGTCCCAC-1" "ACCTAATCGACTTCCT-1" "ACGATCATACATAGAG-1"
#> [49] "ACGCATTCGTGAGTAC-1" "ACGCCAGATGATTTCT-1" "ACGCGGGCCAAGGACA-1"
#> [52] "ACGGAATTTAGCAAAT-1" "ACGTAGATTGCTGATG-1" "ACGTGCGCCTCGTGCA-1"
#> [55] "ACGTTTAGTTGTGATC-1" "ACTACCAGCTCTCTGG-1" "ACTATTCGTCCGTGGT-1"
#> [58] "ACTCAATAAAGGCACG-1" "ACTGCCGTCGTAACTC-1" "ACTGTAGCACTTTGGA-1"
#> [61] "ACTGTCCAGGATTATA-1" "ACTGTCTTCTTTAGAA-1" "ACTGTGCTAGTAGATC-1"
#> [64] "ACTTAGTACGACAAGA-1" "ACTTCGCCATACGCAC-1" "ACTTGGGACCCGGTGG-1"
#> [67] "ACTTTCCTATAGCTTC-1" "AGAACGTGGTACATTC-1" "AGACCATGGGATACAA-1"
#> [70] "AGACCCGCCCTCCTCG-1" "AGACTAGCCTTCCAGA-1" "AGAGCGGGCTAATCAT-1"
#> [73] "AGAGCGTACAAGCTCG-1" "AGATAACTTCAGGGCC-1" "AGATACGACTTCATAT-1"
#> [76] "AGATCTCAGGTGTGAT-1" "AGATGACTCGCCCACG-1" "AGCACCAGTACTCACG-1"
#> [79] "AGCACTTAAGGACGCC-1" "AGCATCGTCGATAATT-1" "AGCCCTAAGCGAAGTT-1"
#> [82] "AGCGACATCCCATTCA-1" "AGCGACCAACGATATT-1" "AGCGGGAAGGGTCCAT-1"
#> [85] "AGCTATTTAATCCAAC-1" "AGGACATCGCACGTCG-1" "AGGCCACCCGTTATGA-1"
#> [88] "AGGCCCATTGTACAGG-1" "AGGCTATGGTTAGCTT-1" "AGGGCGTGATCGGCTA-1"
#> [91] "AGGGCTGCAGTTACAG-1" "AGGGTTTAGTTCGGGA-1" "AGGTAACCTCCTATTC-1"
#> [94] "AGGTACGATATTGCCA-1" "AGGTAGGTACAAAGCT-1" "AGGTTGAGGCACGCTT-1"
#> [97] "AGTAATGTCTTGCCGC-1" "AGTAGGTAACATACAT-1" "AGTATAATACTAGGCA-1"
#> [100] "AGTCAGCCACCGCCTG-1" "AGTCGGCCCAAACGAC-1" "AGTCTTCTCCTCAAAT-1"
#> [103] "AGTTCCTACAGAATTA-1" "AGTTTCGCAGGTCGGA-1" "ATAAAGGCTCGGTCGT-1"
#> [106] "ATAACGGAGTCCAACG-1" "ATAATAGTGTAGGGAC-1" "ATACCACGGGCAACTT-1"
#> [109] "ATACTAGCATGACCCT-1" "ATAGACGAAGAGAAAG-1" "ATAGAGTACTGGGACA-1"
#> [112] "ATAGGGATATCCTTGA-1" "ATAGGTTGGGCAGATG-1" "ATATCTTAGGGCCTTC-1"
#> [115] "ATATTCCCACAGGTCA-1" "ATATTGCTGTCAAAGT-1" "ATATTTAACCCTCAAG-1"
#> [118] "ATCAATCTGGGCTGCA-1" "ATCACTTCATCCTCGC-1" "ATCCAACGCAGTCATA-1"
#> [121] "ATCGACTCTTTCCGTT-1" "ATCGCACGCCGGGAGA-1" "ATCTCCCTGCAATCTA-1"
#> [124] "ATCTGGTTAAGACTGT-1" "ATCTGTAATTGTACCC-1" "ATCTTGACCTGCAACG-1"
#> [127] "ATGAAGCCAAGGAGCC-1" "ATGACGCCGGCTCTAA-1" "ATGAGGAGTGTTAATC-1"
#> [130] "ATGATCGGGAATAGAC-1" "ATGCACTACCGCATTG-1" "ATGCATGATCCAGGAT-1"
#> [133] "ATGCCGGTCTTGCATA-1" "ATGCGACAGTCCCATT-1" "ATGCTCAGTGTTGCAT-1"
#> [136] "ATGGATTGACCAAACG-1" "ATGTGCATCCGACGCA-1" "ATGTTACGAGCAATAC-1"
#> [139] "ATTAATACTACGCGGG-1" "ATTAATTCGGTCACTC-1" "ATTACTAGCCTCTTGC-1"
#> [142] "ATTAGATTGATAGCGG-1" "ATTATGCCATAGGGAG-1" "ATTCCTCCGCCAGTGC-1"
#> [145] "ATTCTCGTCTCTTTAG-1" "ATTGAAGATCTTAGTG-1" "ATTGCTGCTCCTCCAT-1"
#> [148] "ATTGGGAATATCTTGG-1" "ATTTAACTCGTATTAC-1" "ATTTACAGTTTACTGG-1"
#> [151] "ATTTGTTCCAGGGCTC-1" "CAAACGGTCGCACTTT-1" "CAAACTATTGAGCTTC-1"
#> [154] "CAAATTGTCAGCAAGC-1" "CAACGACCCGTTTACA-1" "CAACGGTTCTTGATAC-1"
#> [157] "CAACTCCTTGATCCCG-1" "CAAGCAACGTCGGAGT-1" "CAAGCACCAAATGCCT-1"
#> [160] "CAATAAACCTTGGCCC-1" "CAATTAAGGGTGATGA-1" "CACACAGGGATAGATT-1"
#> [163] "CACAGCACCCACGGCA-1" "CACAGCTAGGGAGTGA-1" "CACCATCGGAGGAGAC-1"
#> [166] "CACCCACACGTCACCC-1" "CACCGCCAGAAGGTTT-1" "CACCTAATCAGTTTAC-1"
#> [169] "CACCTCGATGGTGGAC-1" "CACGAAAGTTAGTCCC-1" "CACGCACAGCGCAGCT-1"
#> [172] "CACGCAGCGAGGCTTT-1" "CACTAAAGTTGCCTAT-1" "CACTCAGCTCTTGAGG-1"
#> [175] "CACTGTCCAAGTGAGA-1" "CACTTAATCAGACGGA-1" "CACTTCGCCACAGGCT-1"
#> [178] "CAGAGCATGAGCTTGC-1" "CAGATACTAACATAGT-1" "CAGCTCACTGAGACAT-1"
#> [181] "CAGCTCGTGCTTGTGT-1" "CAGCTTAGTAGGTAGC-1" "CAGTGTCCGCAGAATG-1"
#> [184] "CAGTTCAAATTGACAC-1" "CATACAAAGCCGAACC-1" "CATAGTAGCATAGTAG-1"
#> [187] "CATCATCTACCCGGAC-1" "CATCGCCCGCGGCCAA-1" "CATGAACCGACATTTG-1"
#> [190] "CATGATGCACAATTCT-1" "CATGCGTTAGACAGAA-1" "CATGCTGGCTCCAATT-1"
#> [193] "CATGGCAGGAAGATCG-1" "CATGGTCTAGATACCG-1" "CATTACGTCGGCCCGT-1"
#> [196] "CATTATGCTTGTTGTG-1" "CCAAACAGAACCCTCG-1" "CCAACGATGCACTGAT-1"
#> [199] "CCAAGACTTCTGCGAA-1" "CCAAGCGTAACTCGTA-1" "CCAAGGAACAGAGAGG-1"
#> [202] "CCAATAGTGCCGTCGA-1" "CCAATTGAATGTTAAT-1" "CCACGAGAAGAGAATC-1"
#> [205] "CCAGGGACGTGGCCTC-1" "CCATAAACAACCCGAC-1" "CCATAGGTTGGCGTGG-1"
#> [208] "CCATCCATACCAAGTC-1" "CCATGCCTGTTTAGTA-1" "CCATGCTCTGCAGGAA-1"
#> [211] "CCATTAGCGATAATCC-1" "CCATTCCCTGCCCACA-1" "CCCGACCATAGTCCGC-1"
#> [214] "CCCGCCATGCTCCCGT-1" "CCCGTCAGCGTCTGAC-1" "CCCTCATTCTGGAATT-1"
#> [217] "CCCTGAAATGAGTTGA-1" "CCGAAAGTGGTGAGCA-1" "CCGCCGGTCAACACAC-1"
#> [220] "CCGGAATGGTTTCAGT-1" "CCGGCGCATATTGGAT-1" "CCGGGACCCGCAGAGA-1"
#> [223] "CCGGGCGGTCTCGTCA-1" "CCGTACCCAAGCGCCA-1" "CCGTGCCCATGACGGC-1"
#> [226] "CCTACGGCTCAGTCGA-1" "CCTACTGCTTACACTT-1" "CCTAGTTAGTCGCATG-1"
#> [229] "CCTATGGGTTACCGTC-1" "CCTCACCAATCTTGAC-1" "CCTCCGACAATTCAAG-1"
#> [232] "CCTCGAAGTGGACGGG-1" "CCTCGCCAGCAAATTA-1" "CCTCTAATCTGCCAAG-1"
#> [235] "CCTCTCTCCCATCTAG-1" "CCTCTGGCCTAGACGG-1" "CCTGAATATTTACATA-1"
#> [238] "CCTGCTATTTGAGAAG-1" "CCTGGCTAGACCCGCC-1" "CCTGTCACCCGGGCTC-1"
#> [241] "CCTTCTTGATCCAGTG-1" "CGAACGCCCAGTGCCG-1" "CGAAGTTGCTCTGTGT-1"
#> [244] "CGAGAGATGTGAACCT-1" "CGAGCGTTGATCAGCC-1" "CGAGCTGGGCTTTAGG-1"
#> [247] "CGAGGCTAAATATGGC-1" "CGCAAACACGAGTTAC-1" "CGCAATTACTTTCGGT-1"
#> [250] "CGCAATTAGGGTAATA-1" "CGCAATTCTACAATAA-1" "CGCATTAGCTAATAGG-1"
#> [253] "CGCGCCCGACTTAATA-1" "CGCGTTCATGAAATAC-1" "CGCTATACCGCCCACT-1"
#> [256] "CGCTATTCAATGTATG-1" "CGCTCGACATAATGAT-1" "CGCTCTCCGTAGATTA-1"
#> [259] "CGCTGTGACGCCGCAC-1" "CGCTTCCACTGAAATC-1" "CGCTTTCATACCGGTG-1"
#> [262] "CGGAGTTTGAGAGACA-1" "CGGCACTCAAGAAAGT-1" "CGGCCACGCACAAAGT-1"
#> [265] "CGGGATCAATGTAAGA-1" "CGGGCAGCTAAACCGC-1" "CGGTGTACTTGATCCC-1"
#> [268] "CGTACCTGATAGGCCT-1" "CGTAGCGAATTGTCAG-1" "CGTATTAAGAGATCTA-1"
#> [271] "CGTCAGTGCGCACAAG-1" "CGTCTGGAAGGGCCCG-1" "CGTGTCCCATTCGCGA-1"
#> [274] "CGTTGTTTCAATTCCC-1" "CGTTTAAGCGGAGCAC-1" "CGTTTCGCTCATTACA-1"
#> [277] "CTAATTCGCACGCGCT-1" "CTAATTTCAACAACAC-1" "CTACGCACGGAGTACC-1"
#> [280] "CTACTGCCACCTGACC-1" "CTAGCATAGTATAATG-1" "CTAGTGAAGGACAGGA-1"
#> [283] "CTAGTTGGGCCCGGTA-1" "CTATCGGGTCTCAACA-1" "CTATGTCACTAGCCCA-1"
#> [286] "CTATGTCTATTGAAAC-1" "CTCAGGACTCACCTGT-1" "CTCATGGCTCACAATC-1"
#> [289] "CTCATTTGATGGGCGG-1" "CTCCGGCCTAATATGC-1" "CTCCTAAGTTATGTCT-1"
#> [292] "CTCGAGGTCGAACAGT-1" "CTCGCACCTATATAGT-1" "CTCGGTCCGTAGCCTG-1"
#> [295] "CTCTCACAATCGATGA-1" "CTCTGCGAAGCAAGCA-1" "CTCTGGACGCCTGGTG-1"
#> [298] "CTCTGTTTGAGGATTC-1" "CTGAAAGAGATCCGAC-1" "CTGCACCTGGAACCGC-1"
#> [301] "CTGGAAATGGATGCTT-1" "CTGTATGGTGTAGAAA-1" "CTGTTCACTGCCTGTG-1"
#> [304] "CTGTTCATCTCACGGG-1" "CTTAACTTCGAAGTAC-1" "CTTACACGGTATTCCA-1"
#> [307] "CTTACACTGGGAAATA-1" "CTTATGTTGACTACCA-1" "CTTCATAGCTCAAGAA-1"
#> [310] "CTTCTTACGTCGTATA-1" "CTTGTACTTGTTGACT-1" "CTTGTTTATGTAGCCA-1"
#> [313] "CTTTAACTTTCAAAGG-1" "CTTTGGCTTTAGTAAA-1" "GAAACAGCCATGCAGT-1"
#> [316] "GAAACTCTAATGAAGG-1" "GAAAGTGACTAACTGC-1" "GAAATCGCGCGCAACT-1"
#> [319] "GAAATGGCGGTGTTAG-1" "GAAATTCACATCGCTG-1" "GAACACACATCAACCA-1"
#> [322] "GAACGACCGAATGATA-1" "GAAGAACGGTGCAGGT-1" "GAAGCGTGAGGAATTT-1"
#> [325] "GAAGCTTGCTGACCGC-1" "GAAGTGCTGGATAGCT-1" "GAATCGACATGGTCAC-1"
#> [328] "GAATCGCCGGACACGG-1" "GAATGTTGGGTAATCT-1" "GAATTATAGTGAAAGG-1"
#> [331] "GAATTTCTCGCTGCAG-1" "GACAACGCAGCTTACG-1" "GACACAAGGGAAGAAA-1"
#> [334] "GACCAGAGCCCTGTAG-1" "GACGCCTGTTGCAGGG-1" "GACGTGTAGGGATTAT-1"
#> [337] "GACTAAGATCATGCAC-1" "GACTAAGTAGGCTCAC-1" "GAGACTGATGGGTAGA-1"
#> [340] "GAGATCTGCTTGGCAT-1" "GAGATCTGTCACTCCG-1" "GAGCATCATCCCTGGG-1"
#> [343] "GAGCGAGGGAGTACCG-1" "GAGCTCTCGGACCTAA-1" "GAGGAATGGAGAGGTT-1"
#> [346] "GAGGCTATCAAAGTCG-1" "GAGGGCATCGCGTATC-1" "GAGGTACATCCATCTT-1"
#> [349] "GAGTACGGGTATACAA-1" "GATAAATCGGTGGATG-1" "GATATCTCATGCAATA-1"
#> [352] "GATCATTCCAAACATT-1" "GATCCCTTTATACTGC-1" "GATCGACACTATCTGA-1"
#> [355] "GATCGGTGGCCATAAC-1" "GATGCTACAAGCGCCT-1" "GATGGCGCACACATTA-1"
#> [358] "GATGTTTGTGCGAGAT-1" "GATTCCCTTGTCGCAG-1" "GATTCCGCGTTTCCGT-1"
#> [361] "GCAAATATTACGCTTT-1" "GCAAGTGCACAGAGAA-1" "GCACTAGTCGCGCTAT-1"
#> [364] "GCAGGACTATAGAATA-1" "GCATCCCTAACTTTGA-1" "GCCCACCAAGGCTGTC-1"
#> [367] "GCCCAGTTGGTATGCC-1" "GCCCGCGCGTTTGACA-1" "GCCGAAATTCCTACGT-1"
#> [370] "GCCTAGCGATCTGACC-1" "GCCTATTCCGATATAG-1" "GCCTTCAGCCCTACCG-1"
#> [373] "GCGAAGCCATACCCGT-1" "GCGAGTTCTGCAAAGA-1" "GCGCTAATTGAATAGA-1"
#> [376] "GCGGGAACCAGGCCCT-1" "GCGGTCCCTAGACGCA-1" "GCGTCGAAATGTCGGT-1"
#> [379] "GCTAATACCGAATGCC-1" "GCTAGTTTCATTGAGG-1" "GCTCTAAACCCTGACG-1"
#> [382] "GCTCTATGTTACGTGC-1" "GCTCTCGGGTACCGAA-1" "GCTGCTCTCCGGACAC-1"
#> [385] "GCTGGCATATTCACCT-1" "GCTTGATGATAATCAG-1" "GGAGAAGTCATTGGCA-1"
#> [388] "GGAGTGCCGCCCTGGA-1" "GGATTCAGTACGGTGG-1" "GGCAATAGTCAATGAG-1"
#> [391] "GGCACTCCACTGGGCA-1" "GGCATACAGGTAGCGG-1" "GGCGGAGTAATATTAG-1"
#> [394] "GGCGGTAGGATCATTG-1" "GGCGTCCTATCCGCTG-1" "GGCTATTAAGTTGTAT-1"
#> [397] "GGCTCGTGCCACCAGC-1" "GGCTCTGCTCCAACGC-1" "GGCTGGCTAGCTTAAA-1"
#> [400] "GGGACTGCATAGATAG-1" "GGGAGAACTCACAGTA-1" "GGGAGTTAATGAGGCG-1"
#> [403] "GGGCGATATGTGTGAA-1" "GGGCGGTCCTATTGTC-1" "GGGCGTACATTTATAT-1"
#> [406] "GGGCTGCCTAGGGCGA-1" "GGGCTGGTTAGTCGCG-1" "GGGTATGTATGCACTT-1"
#> [409] "GGGTCACCGTGACGGT-1" "GGGTGTTTCAGCTATG-1" "GGTAACTATGTATCTG-1"
#> [412] "GGTAGTGCTCGCACCA-1" "GGTATTGCCGAGTTTA-1" "GGTCGGTAATTAGACA-1"
#> [415] "GGTGAGATGCAGATAA-1" "GGTGCGGATAAGTGGC-1" "GGTTAGGCTTGGAGAA-1"
#> [418] "GGTTTACAATCTCAAT-1" "GGTTTGAGTGCTGGAA-1" "GTAAGCGGGCAGTCAG-1"
#> [421] "GTAAGTAGGGTATACC-1" "GTACGAGATTGCGACA-1" "GTACTAAGATTTGGAG-1"
#> [424] "GTACTGAGGTCGTAAC-1" "GTACTGCATGAAGCGT-1" "GTACTTGGGCACTTCT-1"
#> [427] "GTAGACGTCGTTACAT-1" "GTATAGGACTCAGTAG-1" "GTATCAGCTTGGGTTC-1"
#> [430] "GTCAAAGTTTACATAG-1" "GTCACTCTCCAAATCT-1" "GTCAGAATAGTCTATG-1"
#> [433] "GTCATGCACCTCCGTT-1" "GTCATGGACATGACTA-1" "GTCCCAACGTAAAGTA-1"
#> [436] "GTCCGGCTGAATTGCG-1" "GTCGGATATCTCAGAC-1" "GTCGTCAATTATAAGG-1"
#> [439] "GTGAAACGTGCTCCAC-1" "GTGCAACAAATGTGGC-1" "GTGCACGAAAGTGACT-1"
#> [442] "GTGCGGGTCTCCAAAT-1" "GTGCTCAAGTACTGTC-1" "GTGGACGTGCTGAGAC-1"
#> [445] "GTGGGCTTAGACACAC-1" "GTTCACAGGAGTCTAG-1" "GTTCCAGTCTGACCAT-1"
#> [448] "GTTCTTCCCTCGATGT-1" "GTTGCACGGAGTTTCG-1" "GTTGTCGTGTTAGTTG-1"
#> [451] "GTTTCCTGGAGGGTGA-1" "GTTTGACCAAATCCTA-1" "GTTTGGCCGCTCAGCG-1"
#> [454] "TAAATGAATCCGTTTC-1" "TAACAAAGGGAGAAGC-1" "TAACGCTTTGAGAGCG-1"
#> [457] "TAACTATCGAAGGTCC-1" "TAACTCCATGGAGGCT-1" "TAAGGAACTTGTGGGA-1"
#> [460] "TAAGGCAACATAAGAT-1" "TAATACACAGTAGTAT-1" "TAATATTGAAATTCGC-1"
#> [463] "TACAAGTCTCGTGCAT-1" "TACCAGCTAGGTTTAA-1" "TACCTCACGCTTGTAC-1"
#> [466] "TACGAACACGACTTCA-1" "TACGAGAACTTCACGT-1" "TACGATGTTGATCATC-1"
#> [469] "TACGTGCACTATGCTG-1" "TAGAGCTACGAAGAAC-1" "TAGAGTCTAAGCGAAC-1"
#> [472] "TAGCTAAGTCCGGGAG-1" "TAGGGTGTTTCAAGAG-1" "TAGGTGAGCCCTACTC-1"
#> [475] "TAGGTTCGAGTTCGTC-1" "TAGTGCCCTCCAGAGT-1" "TAGTTTATTCTTGCTT-1"
#> [478] "TATAAATCCACAAGCT-1" "TATAAGTGAGGATAGC-1" "TATACACGCAAAGTAT-1"
#> [481] "TATCCATATCATGCGA-1" "TATCCTGCATGGGAAT-1" "TATCGATGATTAAACG-1"
#> [484] "TATGCTCCCTACTTAC-1" "TATGGATGTGCTACGC-1" "TATGGCCCGGCCTCGC-1"
#> [487] "TATGGGTACGTATCGT-1" "TATTCAATTCTAATCC-1" "TATTCGTGCCAGAATA-1"
#> [490] "TATTTAGTCTAGATCG-1" "TATTTGTTACCCTTTA-1" "TCAAACAACCGCGTCG-1"
#> [493] "TCAAACTTAGATTGTT-1" "TCAACACATTGGGTAA-1" "TCAACCATGTTCGGGC-1"
#> [496] "TCACAGGTTATTGGGC-1" "TCACGCATTGTAGATC-1" "TCACGGTCATCGCACA-1"
#> [499] "TCAGCAAATGCATCTC-1" "TCAGGGTGTAACGTAA-1" "TCAGGTTCTTTGAGAA-1"
#> [502] "TCAGTACTGACCCGCG-1" "TCATCACTCGAGCTCG-1" "TCATCCCAGAGGGTGG-1"
#> [505] "TCCACAATGGTTTACG-1" "TCCAGGCGAGTACGGT-1" "TCCCAAAGACGAAGGA-1"
#> [508] "TCCCAGCTTTAGTCTG-1" "TCCCAGGCTTAGCTAA-1" "TCCCGCGTACTCCTGG-1"
#> [511] "TCCCGGGTGTGCTGCT-1" "TCCCGTCAGTCCCGCA-1" "TCCCTGGCTCGCTGGA-1"
#> [514] "TCCGATAATTGCCATA-1" "TCCGATGACTGAGCTC-1" "TCCGATGGTGCGACAT-1"
#> [517] "TCCGATTACATTGCCG-1" "TCCTCTACGAGATGGC-1" "TCCTTCAGTGGTCGAA-1"
#> [520] "TCCTTTCTTACGCTTA-1" "TCGAAATTTAGGACCA-1" "TCGCATCCCTAAGTGT-1"
#> [523] "TCGCCGGTCGATCCGT-1" "TCGCGTCCAGAAGGTC-1" "TCGCTCGATATATTCC-1"
#> [526] "TCGCTGGGCGGATTGT-1" "TCGCTGTGCGTAAATC-1" "TCGGAATGCGCTCTGA-1"
#> [529] "TCGGAGTACATGAGTA-1" "TCGTATAGTGCAATTA-1" "TCGTCCGCTGGCGTCT-1"
#> [532] "TCTACCGTCCACAAGC-1" "TCTAGCATCTTCGATG-1" "TCTAGTTATCAGAAGA-1"
#> [535] "TCTATCATGCAGTTAC-1" "TCTATCGGTCGCAACA-1" "TCTATTACGCTGGCGA-1"
#> [538] "TCTCTAATAGCTGGTA-1" "TCTGAACCGGTCGGCT-1" "TCTTACAGAGGTACCG-1"
#> [541] "TCTTACGGCATCCGAC-1" "TCTTCGATACCAATAA-1" "TCTTGATGCGTAGCGA-1"
#> [544] "TCTTGGTAACACCAAA-1" "TGAAACTTATGCAAGC-1" "TGACCCACGTTAGACA-1"
#> [547] "TGAGAATGCTTTACCG-1" "TGATCGGTTTGACCCT-1" "TGATCTCCGGCGCCAG-1"
#> [550] "TGATTCGTCTATCACT-1" "TGATTTCCTCCTGACG-1" "TGCAAGAATGACGTAA-1"
#> [553] "TGCAGGATCGGCAAAG-1" "TGCATGGATCGGATCT-1" "TGCCACCTGGCGAAAC-1"
#> [556] "TGCCTGATCAAACGAT-1" "TGCGCAAAGCATTTGG-1" "TGCGCGATTAACGGAG-1"
#> [559] "TGCGGAGTAAAGGTGC-1" "TGCGGCATAGTTCAAC-1" "TGCGGTGAAATTTCAT-1"
#> [562] "TGCTGGTTGGACAATT-1" "TGGAAGACGAACACCA-1" "TGGAAGGATAAAGATG-1"
#> [565] "TGGAGTGATGCGATGA-1" "TGGCCAAACTGAAGTA-1" "TGGCCGTATATTGACC-1"
#> [568] "TGGCTTTGGGTAGACA-1" "TGGGAAATGCCTTTCC-1" "TGGGCACGTTCTATGG-1"
#> [571] "TGGGCCACAAGAGCGC-1" "TGGTTCGTAGCAAAGG-1" "TGTAGTGATCTATAAT-1"
#> [574] "TGTCCCGACATAGCAC-1" "TGTCCTAAGTCACCGC-1" "TGTCTACAGTTTCTGT-1"
#> [577] "TGTGACTACGCCAGTC-1" "TGTGTCGCGAGTTGCA-1" "TGTTCTTCCATTGACT-1"
#> [580] "TGTTTCGGTACTTCTC-1" "TTAACCAACCCTCCCT-1" "TTAAGCGCCTGACCCA-1"
#> [583] "TTAATCAGTACGTCAG-1" "TTAATGTAGACCAGGT-1" "TTAATTTCAGACGCGG-1"
#> [586] "TTACAACTACGCATCC-1" "TTACATCGTGGCCTGG-1" "TTACCATTGATTACCC-1"
#> [589] "TTAGCAACATGGATGT-1" "TTATATTTGGCAATCC-1" "TTATCCAATCGAACTC-1"
#> [592] "TTATCTGTATCATAAC-1" "TTATGACAAACTGGAT-1" "TTATTAGGGAAGCATC-1"
#> [595] "TTCAAAGTCTCTAGCC-1" "TTCAACGACCCGACCG-1" "TTCAAGCCGAGCTGAG-1"
#> [598] "TTCATGGCGCAACAGG-1" "TTCCTCGAGGGTGTCT-1" "TTCGACGGGAAGGGCG-1"
#> [601] "TTCGCACTCGCGTGCT-1" "TTCGTACTCCAGAACG-1" "TTCTACTTGCGAGGGC-1"
#> [604] "TTCTAGGCCAATTGTG-1" "TTCTTAGTGAACGGTG-1" "TTCTTAGTGGCTCAGA-1"
#> [607] "TTCTTGTAACCTAATG-1" "TTGAAGAATTCCCAGG-1" "TTGAATATGGACTTTC-1"
#> [610] "TTGATCTAACTTTGTC-1" "TTGATTATGCAGATGA-1" "TTGCACGGAGCAGCAC-1"
#> [613] "TTGCTCCCATACCGGA-1" "TTGCTGAAGGAACCAC-1" "TTGCTGATCATGTTCG-1"
#> [616] "TTGGATTGGGTACCAC-1" "TTGGCTCGCATGAGAC-1" "TTGGGACACTGCCCGC-1"
#> [619] "TTGGGCGGCGGTTGCC-1" "TTGTAATCCGTACTCG-1" "TTGTATCACACAGAAT-1"
#> [622] "TTGTCGTTCAGTTACC-1" "TTGTGGCCCTGACAGT-1" "TTGTTCAGTGTGCTAC-1"
spatIDs(g, subset = nr_feats <= 200)
#> [1] "GTCGTCAATTATAAGG-1" "TCGTATAGTGCAATTA-1" "GAGTACGGGTATACAA-1"
#> [4] "TCTTACAGAGGTACCG-1" "GTTGTCGTGTTAGTTG-1" "GTACTTGGGCACTTCT-1"
#> [7] "CGCTATTCAATGTATG-1" "AATGGTTCTCACAAGC-1" "CTTCATAGCTCAAGAA-1"
#> [10] "CAACGGTTCTTGATAC-1" "ACACCCGAGAAATCCG-1" "CACTGTCCAAGTGAGA-1"
#> [13] "CATAGTAGCATAGTAG-1" "CAACTCCTTGATCCCG-1" "AAGTAGAAGACCGGGT-1"
#> [16] "TACGTGCACTATGCTG-1" "GTATCAGCTTGGGTTC-1" "TAACAAAGGGAGAAGC-1"
#> [19] "TTACATCGTGGCCTGG-1" "TCTGAACCGGTCGGCT-1" "TATAAGTGAGGATAGC-1"
#> [22] "TGCTGGTTGGACAATT-1" "TATAAATCCACAAGCT-1" "CGCTCGACATAATGAT-1"
#> [25] "TTCAACGACCCGACCG-1" "GTCACTCTCCAAATCT-1" "TTCTACTTGCGAGGGC-1"
#> [28] "CTGTTCATCTCACGGG-1" "TTCTTGTAACCTAATG-1" "GCTTGATGATAATCAG-1"
#> [31] "TTGGCTCGCATGAGAC-1" "GCCCAGTTGGTATGCC-1" "TCGTCCGCTGGCGTCT-1"
#> [34] "TTCTAGGCCAATTGTG-1" "ATGAAGCCAAGGAGCC-1" "CCCGTCAGCGTCTGAC-1"
#> [37] "GACTAAGATCATGCAC-1" "TGGTTCGTAGCAAAGG-1" "CTGTTCACTGCCTGTG-1"
#> [40] "CGTACCTGATAGGCCT-1" "GAATGTTGGGTAATCT-1" "CACACAGGGATAGATT-1"
#> [43] "TAACTATCGAAGGTCC-1" "GGGCGTACATTTATAT-1" "ATCGCACGCCGGGAGA-1"
#> [46] "TATGCTCCCTACTTAC-1" "TCCTCTACGAGATGGC-1" "TTGATTATGCAGATGA-1"
#> [49] "GTAAGTAGGGTATACC-1" "CGCAAACACGAGTTAC-1" "TGGCCGTATATTGACC-1"
#> [52] "ACTGTAGCACTTTGGA-1" "GCTCTCGGGTACCGAA-1" "CACCGCCAGAAGGTTT-1"
#> [55] "TCCCAAAGACGAAGGA-1" "TTATATTTGGCAATCC-1" "AGCACCAGTACTCACG-1"
#> [58] "CGTGTCCCATTCGCGA-1" "GATCCCTTTATACTGC-1" "ATAGGTTGGGCAGATG-1"
#> [61] "CAATTAAGGGTGATGA-1" "TCGCGTCCAGAAGGTC-1" "GGCGTCCTATCCGCTG-1"
#> [64] "TCAGCAAATGCATCTC-1" "GAGATCTGTCACTCCG-1" "CAGCTTAGTAGGTAGC-1"
#> [67] "CGAAGTTGCTCTGTGT-1" "CTCTGGACGCCTGGTG-1" "AGGGTTTAGTTCGGGA-1"
#> [70] "CTCTCACAATCGATGA-1" "TCGGAGTACATGAGTA-1" "TTACCATTGATTACCC-1"
#> [73] "CCTCTCTCCCATCTAG-1" "GCGCTAATTGAATAGA-1" "GGTAGTGCTCGCACCA-1"
#> [76] "AAGCTCGTGCCAAGTC-1"
spatIDs(g, subset = Dim.1 > 25, dim_reduction_to_use = "umap")
#> [1] "AAATGGTCAATGTGCC-1" "AAATTAACGGGTAGCT-1" "AAGGCTGTGCTCATCG-1"
#> [4] "ACCACAAGTTTCTATC-1" "ACCTAATCGACTTCCT-1" "ACTTGGGACCCGGTGG-1"
#> [7] "AGTTCCTACAGAATTA-1" "ATATTTAACCCTCAAG-1" "ATTGAAGATCTTAGTG-1"
#> [10] "CAAACGGTCGCACTTT-1" "CAGCTCACTGAGACAT-1" "CCAACGATGCACTGAT-1"
#> [13] "CCATTCCCTGCCCACA-1" "CCTCCGACAATTCAAG-1" "CGAAGTTGCTCTGTGT-1"
#> [16] "CGCTCTCCGTAGATTA-1" "CGGGCAGCTAAACCGC-1" "CGTTTCGCTCATTACA-1"
#> [19] "CTTACACGGTATTCCA-1" "CTTTGGCTTTAGTAAA-1" "GAAATGGCGGTGTTAG-1"
#> [22] "GAAGCTTGCTGACCGC-1" "GCAGGACTATAGAATA-1" "GGCACTCCACTGGGCA-1"
#> [25] "GGGCTGGTTAGTCGCG-1" "GTTCACAGGAGTCTAG-1" "TACGAACACGACTTCA-1"
#> [28] "TACGAGAACTTCACGT-1" "TATGGGTACGTATCGT-1" "TCCAGGCGAGTACGGT-1"
#> [31] "TCCCAGCTTTAGTCTG-1" "TCGAAATTTAGGACCA-1" "TTGATCTAACTTTGTC-1"
featIDs(g)
#> [1] "Gna12" "Ccnd2" "Btbd17" "Sox9"
#> [5] "Sez6" "Serpinf1" "S100a6" "Col1a1"
#> [9] "Vwf" "Esam" "Npas1" "Tiam1"
#> [13] "Bcam" "Hmgn2" "Rab3b" "Inmt"
#> [17] "Ddr1" "Homer3" "Cp" "Calb2"
#> [21] "Man1a" "Efnb3" "Hlf" "Gstm7"
#> [25] "Cavin1" "Sst" "Hapln2" "Hspb1"
#> [29] "Ndrg1" "Nid1" "Kit" "Pvalb"
#> [33] "Tmbim1" "Crip1" "Tek" "Elovl1"
#> [37] "Cyba" "Itih3" "Cnp" "Hap1"
#> [41] "Clic1" "Stx1a" "Arpp19" "Dio2"
#> [45] "Id3" "Crlf1" "Ttc9b" "Carhsp1"
#> [49] "Cabp7" "Fam163b" "Rarres2" "Syn2"
#> [53] "Ick" "Prox1" "Adssl1" "Vipr2"
#> [57] "Gltp" "Amotl1" "Bcas1" "Aldh1a2"
#> [61] "Tppp3" "Sirt2" "Lpl" "Cers2"
#> [65] "Qdpr" "Stk32c" "Lbp" "Hsd11b1"
#> [69] "Vtn" "Stac2" "Plxdc1" "Igfbp4"
#> [73] "Dbndd2" "Pltp" "Slc12a4" "Cadps2"
#> [77] "Erbb3" "Pmp22" "Kcnab3" "Myh11"
#> [81] "Plod1" "Etnppl" "Arhgef25" "Rcn3"
#> [85] "Vip" "Utrn" "Grm1" "Reep3"
#> [89] "Fabp7" "Dcn" "Slc17a8" "Dusp6"
#> [93] "Kitl" "Ccn2" "Timp3" "Ascl1"
#> [97] "Unc5b" "Vsir" "Gamt" "Ptprb"
#> [101] "Csrp2" "Adarb1" "Rnf130" "Nefh"
#> [105] "Aebp1" "Sept4" "Gria1" "Sypl"
#> [109] "Arsg" "Cacng4" "Rab37" "Itgb4"
#> [113] "Aspa" "Cygb" "Rflnb" "Doc2b"
#> [117] "Gfap" "Npas3" "Serpina3n" "Clmn"
#> [121] "Prkch" "Fbln5" "Akr1c18" "Gng4"
#> [125] "Sema4d" "Cxcl14" "Hexb" "Iqgap2"
#> [129] "Crhbp" "Rab3c" "Thbs4" "Serinc5"
#> [133] "Erbin" "Prkcd" "Pdlim2" "Ednrb"
#> [137] "Cpne6" "Sema5a" "Matn2" "Nptxr"
#> [141] "Enpp2" "Efcab6" "Ppp1r1a" "Litaf"
#> [145] "Il1rap" "Apod" "Cpox" "Grik1"
#> [149] "Clic6" "Nr4a1" "Igfbp6" "Sncg"
#> [153] "Gzma" "Grm2" "Prph" "Rsph1"
#> [157] "Sox8" "Fam234a" "Lims2" "Aqp4"
#> [161] "Slc12a2" "Cd74" "Pdgfrb" "Csf1r"
#> [165] "Cbln2" "Frmd8" "Gldc" "Tcf7l2"
#> [169] "Bhlhe22" "Kcnip2" "Alas2" "Gdf11"
#> [173] "Baiap2" "Ifitm3" "Phkg1" "Nptx1"
#> [177] "Pde8a" "Itih5" "Homer2" "Fam20c"
#> [181] "Cplx2" "Myo5b" "Snca" "Col3a1"
#> [185] "Ecrg4" "Map4k4" "2010300C02Rik" "Ogfrl1"
#> [189] "Fn1" "Efhd1" "Ngef" "Bok"
#> [193] "Tmem163" "Lct" "Cfh" "Ptpn4"
#> [197] "Tnni1" "Csrp1" "Nfasc" "Syt2"
#> [201] "Atp2b4" "Rgs16" "Ncf2" "Cnih3"
#> [205] "Tmem63a" "Cfap126" "Meig1" "Ccdc3"
#> [209] "Rgs5" "Enkur" "Myoc" "Vim"
#> [213] "Prkcq" "Gad2" "Lcn2" "Nr4a2"
#> [217] "Ermn" "Fibcd1" "Gsn" "Grb14"
#> [221] "Notch1" "Ube2l6" "Gatm" "Cd82"
#> [225] "Mdk" "Lamp5" "Itpka" "Chgb"
#> [229] "Mal" "Pdyn" "Nkx2-2" "Edn3"
#> [233] "Car2" "Col9a3" "Chrna4" "Gss"
#> [237] "Slc7a11" "Tm4sf1" "Kcnab1" "Shox2"
#> [241] "Serpini1" "Tspan2" "S100a11" "Vcam1"
#> [245] "Lef1" "Npy2r" "F3" "Calb1"
#> [249] "Epha7" "Slc44a1" "1110017D15Rik" "Tpm2"
#> [253] "Slc6a9" "Laptm5" "Sema3c" "Hpca"
#> [257] "Padi2" "Slc4a2" "Gabrd" "Rgs12"
#> [261] "Slc30a3" "Emilin1" "1700001C02Rik" "Gabra4"
#> [265] "Pdgfra" "Epha5" "Tesc" "Pitpnm2"
#> [269] "Mmp17" "Cit" "Foxp2" "Arpc1b"
#> [273] "Col1a2" "Eln" "Pcolce" "Tsc22d4"
#> [277] "Cald1" "Ccdc136" "Npy" "Slc13a4"
#> [281] "Gkn3" "Slc6a13" "Mgp" "Lmo3"
#> [285] "Slco1c1" "Cpne9" "Itpr2" "Slc6a11"
#> [289] "Vamp1" "Cd9" "Pglyrp1" "Slc17a6"
#> [293] "Sipa1l3" "Sh3gl3" "Plekhb1" "Nupr1"
#> [297] "Dkk3" "Cox6a2" "Dkkl1" "Fgfr2"
#> [301] "Crym" "Slc38a5" "Flna" "Bgn"
#> [305] "Col4a1" "Plat" "Nr3c2" "Cbln1"
#> [309] "Gab1" "Pllp" "Necab2" "Dbndd1"
#> [313] "Agt" "Cryab" "Tagln" "Mcam"
#> [317] "Olfm2" "Icam5" "Anxa2" "Rora"
#> [321] "Calml4" "Htr3a" "Paqr5" "Rasgrf1"
#> [325] "Zic1" "Mobp" "Hhatl" "Trf"
#> [329] "Cpne4" "Cdhr4" "Cd59a" "Gng11"
#> [333] "Chrm1" "Prr5l" "Ugt8a" "Rims3"
#> [337] "Sgpp2" "Camkv" "Sox10" "Micall1"
#> [341] "Tie1" "Fa2h" "Ucp2" "Vav3"
#> [345] "Ccp110" "Gria2" "Rasl10a" "Foxj1"
#> [349] "Trim59" "Dynlrb2" "Gjc1" "Neurod1"
#> [353] "Ttyh2" "Cpne7" "Nrip3" "Tbr1"
#> [357] "Lcat" "Tmem98" "Myo1d" "Prdm8"
#> [361] "Tgfbi" "Kcnc2" "Thrsp" "Isg15"
#> [365] "Acta2" "H2-Q4" "Dock4" "Myrf"
#> [369] "Lmo1" "Igfbp7" "P2ry12" "Pcdh8"
#> [373] "Lgi4" "Fxyd1" "Fxyd7" "Mag"
#> [377] "Zcchc12" "Anln" "Wnt4" "C1ql2"
#> [381] "Unc93b1" "Tspan15" "Ppp1r14a" "Clic4"
#> [385] "Galnt6" "Ccn3" "Rims2" "Zmat4"
#> [389] "Cldn11" "Ccdc33" "Slc32a1" "Tgm2"
#> [393] "Vstm2l" "Neurod6" "Crygn" "Enpp6"
#> [397] "Neurod2" "Satb2" "Pcp4l1" "Txnip"
#> [401] "Egr1" "Otud7b" "Car14" "Rgs4"
#> [405] "Dock10" "Lpar1" "Trps1" "Ptpn3"
#> [409] "Lefty1" "Zfhx3" "St6galnac5" "Ak5"
#> [413] "Hrh3" "Nexn" "Adgrl4" "Rlbp1"
#> [417] "Igfbp2" "Wfs1" "Cplx3" "Orai2"
#> [421] "Olig2" "Gpr37" "Plcb4" "Nxph4"
#> [425] "Ndufa4l2" "Cacng5" "Plekhg1" "Cmtm5"
#> [429] "Gpr161" "Rfx3" "Igsf21" "Ramp3"
#> [433] "Arhgap12" "Nkx6-2" "Ninj2" "Cldn5"
#> [437] "Htr2c" "Hspb8" "Fmod" "Prelp"
#> [441] "Mpped1" "Rapgef5" "Vwa1" "Stab1"
#> [445] "Arl15" "Reln" "Mustn1" "Pbxip1"
#> [449] "Dnali1" "Id1" "Lrrtm3" "Tmem212"
#> [453] "Epop" "Gjc2" "1190005I06Rik" "Ctla2a"
#> [457] "Cnr1" "Gpr4" "Sowaha" "Tent5c"
#> [461] "Serpinb1a" "S1pr5" "Penk" "Cdc42ep2"
#> [465] "Slitrk6" "Hpcal4" "Olig1" "Rprml"
#> [469] "Stxbp6" "Hs3st2" "Rbp1" "Ppm1e"
#> [473] "Sox18" "Kctd4" "Nxph3" "Vat1l"
#> [477] "Cd24a" "Odf3b" "Gjb1" "Selplg"
#> [481] "Bcl11b" "Lhfp" "Ranbp3l" "Msx1"
#> [485] "Zdhhc22" "Phldb1" "Ctxn1" "Tprn"
#> [489] "Vstm2a" "Ndnf" "Pdp1" "Scn3b"
#> [493] "Cdc42ep1" "Gal3st1" "Rasd1" "Spink8"
#> [497] "Opalin" "Gja4" "Synpo2" "Pcdh20"
#> [501] "Adra1b" "Fam131a" "Tmem125" "Mb21d2"
#> [505] "Lingo3" "Ncald" "Siglech" "Rgs14"
#> [509] "Gm14964" "Gpr17" "Cx3cr1" "Ezr"
#> [513] "Adarb2" "Cpne8" "Plekhg3" "Lamb2"
#> [517] "Creb5" "Cntn2" "Aldh1a1" "Phgdh"
#> [521] "Tnfaip6" "Camk2d" "Shisa6" "Cthrc1"
#> [525] "Tmem119" "Hmgb2" "Tmem158" "Dsp"
#> [529] "Lrtm2" "Gabra5" "Tns1" "Nell1"
#> [533] "Slain1" "Prr18" "S100a8" "S100a9"
#> [537] "Col8a2" "Synpr" "Sertm1" "Adgrf5"
#> [541] "Capg" "Gjc3" "Fcer1g" "Pde1a"
#> [545] "Tafa1" "Ddn" "Hopx" "Ptk2b"
#> [549] "Rgs3" "Kcng2" "Ntng1" "H2-Q7"
#> [553] "Ifitm2" "Plaat3" "Plekhh1" "Myl4"
#> [557] "H2-K1" "Dpp6" "Tmem91" "Cyp2d22"
#> [561] "Ttr" "Suclg2" "Patj" "Btbd3"
#> [565] "Unc13c" "Syt9" "Shisal1" "Grm4"
#> [569] "Sox11" "Slc22a8" "Slc24a3" "Klk8"
#> [573] "Ipcef1" "Tnnt1" "Hhip" "Spag8"
#> [577] "Fxyd6" "Ppp1r3c" "Cbln4" "Nnat"
#> [581] "Myl9" "Vxn" "Lgals1" "Gpr88"
#> [585] "Ctxn3" "Lyz2" "Tmem100" "Wfdc17"
#> [589] "Ahnak" "Hba-a2" "Hba-a1" "Ccdc153"
#> [593] "Ccnd1" "Serpinh1" "Gad1" "Arhgef10"
#> [597] "2410004P03Rik" "Nt5dc2" "Cebpd" "Sod3"
#> [601] "H2-D1" "C4b" "Tmem88b" "Hbb-bt"
#> [605] "Rhog" "Rprm" "Ly6a" "Mog"
#> [609] "Trbc2" "Igkc" "Smim1" "Hs3st4"
#> [613] "Evi2a" "Prkcg" "Ly6c1" "Gbp4"
#> [617] "Wipf3" "BC039966" "Gm13889" "Plcxd2"
#> [621] "Mia" "Pou3f1" "Lrrc10b" "Apol11b"
#> [625] "Gpr62" "Shisa8" "Gm2115" "Kctd12"
#> [629] "1700047M11Rik" "Lhfpl3" "C030029H02Rik" "Gm19935"
#> [633] "9630013A20Rik" "2900040C04Rik"
featIDs(g, subset = nr_cells < 100)
#> [1] "Col1a1" "Inmt" "Cp" "Nid1"
#> [5] "Vipr2" "Aldh1a2" "Lbp" "Myh11"
#> [9] "Dcn" "Slc17a8" "Ascl1" "Aebp1"
#> [13] "Fbln5" "Akr1c18" "Efcab6" "Clic6"
#> [17] "Sncg" "Gzma" "Prph" "Rsph1"
#> [21] "Cd74" "Col3a1" "Ncf2" "Cfap126"
#> [25] "Meig1" "Enkur" "Myoc" "Lcn2"
#> [29] "Edn3" "1110017D15Rik" "Tpm2" "Emilin1"
#> [33] "1700001C02Rik" "Col1a2" "Eln" "Pcolce"
#> [37] "Slc13a4" "Gkn3" "Slc6a13" "Nupr1"
#> [41] "Slc38a5" "Tagln" "Calml4" "Htr3a"
#> [45] "Paqr5" "Cdhr4" "Tie1" "Foxj1"
#> [49] "Dynlrb2" "Gjc1" "Tgfbi" "H2-Q4"
#> [53] "Ccdc33" "Tgm2" "Crygn" "Nexn"
#> [57] "Nxph4" "Fmod" "Stab1" "Mustn1"
#> [61] "Dnali1" "Tmem212" "Gpr4" "Tent5c"
#> [65] "Slitrk6" "Odf3b" "Ranbp3l" "Msx1"
#> [69] "Ndnf" "Gja4" "Gm14964" "Dsp"
#> [73] "S100a8" "S100a9" "Col8a2" "Capg"
#> [77] "H2-Q7" "Hhip" "Spag8" "Ctxn3"
#> [81] "Wfdc17" "Ccdc153" "2410004P03Rik" "Igkc"
#> [85] "Gbp4" "BC039966" "Mia" "Apol11b"
#> [89] "Shisa8" "C030029H02Rik" "Gm19935" "9630013A20Rik"
#> [93] "2900040C04Rik"
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"