This function combines the cell metadata with spatial locations and enrichment results from runSpatialEnrich.
Usage
combineMetadata(
gobject,
spat_unit = NULL,
feat_type = NULL,
spat_loc_name = "raw",
spat_enr_names = NULL,
verbose = TRUE
)Examples
g <- GiottoData::loadGiottoMini("visium")
#> 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"
combineMetadata(g)
#> Key: <cell_ID>
#> cell_ID in_tissue nr_feats perc_feats total_expr leiden_clus
#> <char> <int> <int> <num> <num> <num>
#> 1: AAAGGGATGTAGCAAG-1 1 227 35.80442 995.1491 1
#> 2: AAATGGCATGTCTTGT-1 1 283 44.63722 1123.8751 2
#> 3: AAATGGTCAATGTGCC-1 1 248 39.11672 1027.6322 4
#> 4: AAATTAACGGGTAGCT-1 1 222 35.01577 974.3766 4
#> 5: AACAACTGGTAGTTGC-1 1 313 49.36909 1174.4881 6
#> ---
#> 620: TTGTAATCCGTACTCG-1 1 315 49.68454 1184.0178 4
#> 621: TTGTATCACACAGAAT-1 1 240 37.85489 999.6419 2
#> 622: TTGTCGTTCAGTTACC-1 1 220 34.70032 994.6648 1
#> 623: TTGTGGCCCTGACAGT-1 1 204 32.17666 930.5489 5
#> 624: TTGTTCAGTGTGCTAC-1 1 237 37.38170 1034.8893 1
#> custom_leiden sdimx sdimy
#> <num> <int> <int>
#> 1: 1 5477 -4125
#> 2: 3 5959 -2808
#> 3: 2 4720 -5202
#> 4: 2 5202 -5322
#> 5: 2 4101 -4604
#> ---
#> 620: 2 4996 -5442
#> 621: 3 6303 -2688
#> 622: 1 5202 -3885
#> 623: 1 5340 -3406
#> 624: 1 5615 -4125