Combine cell metadata with spatial cell information (e.g. polygon)
Details
The returned data.table has the following columns:
sdimx: spatial feature location on the x-axis
sdimy: spatial feature location on the y-axis
cell_ID: unique cell ID
feat: selected feature(s)
other columns that are part of the cell metadata
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"
combineSpatialCellMetadataInfo(g, spat_unit = "aggregate", feat_type = "rna")
#> $rna
#> Key: <cell_ID>
#> cell_ID stack agg_n valid nr_feats
#> <char> <char> <num> <int> <int>
#> 1: 100210519278873141813371229408401071444 <NA> 2 1 22
#> 2: 101161259912191124732236989250178928032 <NA> 2 1 36
#> 3: 101488859781016188084173008420811094152 <NA> 2 1 35
#> 4: 101523780333017320796881555775415156847 <NA> 2 1 39
#> 5: 102184699197574201819246996094734116255 <NA> 2 1 44
#> ---
#> 458: 9677424102111816817518421117250891895 <NA> 2 1 30
#> 459: 97068595823890802071024838798130036179 <NA> 2 1 46
#> 460: 97411078642927912684859796714759494710 <NA> 2 1 33
#> 461: 9816437869021910185567097363182418837 <NA> 2 1 31
#> 462: 98561957902191275233320065611022298397 <NA> 2 1 53
#> perc_feats total_expr leiden_clus louvain_clus feat
#> <num> <num> <num> <num> <char>
#> 1: 6.528190 163.6923 4 15 rna
#> 2: 10.682493 228.7269 2 10 rna
#> 3: 10.385757 242.0458 1 22 rna
#> 4: 11.572700 262.3842 1 24 rna
#> 5: 13.056380 291.5877 2 0 rna
#> ---
#> 458: 8.902077 211.7179 2 3 rna
#> 459: 13.649852 279.5605 2 5 rna
#> 460: 9.792285 226.7092 4 15 rna
#> 461: 9.198813 220.4129 3 13 rna
#> 462: 15.727003 326.0539 1 26 rna
#>