combine feature data information
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"
combineFeatureData(g, spat_unit = "aggregate", feat_type = "rna")
#> $rna
#> Key: <feat_ID>
#> feat_ID nr_cells perc_cells total_expr mean_expr mean_expr_det hvg_orig
#> <char> <int> <num> <num> <num> <num> <char>
#> 1: Abcc9 10 2.164502 71.39463 0.15453382 7.139463 no
#> 2: Abcc9 10 2.164502 71.39463 0.15453382 7.139463 no
#> 3: Abcc9 10 2.164502 71.39463 0.15453382 7.139463 no
#> 4: Abcc9 10 2.164502 71.39463 0.15453382 7.139463 no
#> 5: Abcc9 10 2.164502 71.39463 0.15453382 7.139463 no
#> ---
#> 79757: Vmn2r1 7 1.515152 41.22525 0.08923213 5.889321 no
#> 79758: Vmn2r1 7 1.515152 41.22525 0.08923213 5.889321 no
#> 79759: Vmn2r1 7 1.515152 41.22525 0.08923213 5.889321 no
#> 79760: Vmn2r1 7 1.515152 41.22525 0.08923213 5.889321 no
#> 79761: Vmn2r1 7 1.515152 41.22525 0.08923213 5.889321 no
#> var hvf geom part x y hole global_z
#> <num> <char> <int> <num> <num> <num> <num> <int>
#> 1: 3.2630074 yes 52 1 6401.822 -5074.172 0 0
#> 2: 3.2630074 yes 1405 1 6434.212 -4994.575 0 0
#> 3: 3.2630074 yes 1524 1 6435.822 -4993.068 0 0
#> 4: 3.2630074 yes 1564 1 6436.190 -4993.599 0 0
#> 5: 3.2630074 yes 1568 1 6436.225 -4994.331 0 0
#> ---
#> 79757: 0.9765725 no 55606 1 6755.787 -4842.521 0 1
#> 79758: 0.9765725 no 64289 1 6788.817 -4766.861 0 1
#> 79759: 0.9765725 no 64391 1 6789.242 -4927.838 0 1
#> 79760: 0.9765725 no 65159 1 6792.122 -4894.507 0 1
#> 79761: 0.9765725 no 77586 1 6876.786 -5032.958 0 1
#> feat_ID_uniq feat spat_unit
#> <int> <char> <char>
#> 1: 52 rna aggregate
#> 2: 1414 rna aggregate
#> 3: 1534 rna aggregate
#> 4: 1574 rna aggregate
#> 5: 1578 rna aggregate
#> ---
#> 79757: 56040 rna aggregate
#> 79758: 64767 rna aggregate
#> 79759: 64870 rna aggregate
#> 79760: 65645 rna aggregate
#> 79761: 78156 rna aggregate
#>