Combine cell cell communication tables

Combine spatial and expression based cell-cell communication data.tables

combCCcom(
  spatialCC,
  exprCC,
  min_lig_nr = 3,
  min_rec_nr = 3,
  min_padj_value = 1,
  min_log2fc = 0,
  min_av_diff = 0,
  detailed = FALSE
)

Arguments

spatialCC

spatial cell-cell communication scores

exprCC

expression cell-cell communication scores

min_lig_nr

minimum number of ligand cells

min_rec_nr

minimum number of receptor cells

min_padj_value

minimum adjusted p-value

min_log2fc

minimum log2 fold-change

min_av_diff

minimum average expression difference

detailed

detailed option used with spatCellCellcom (default = FALSE)

Value

combined data.table with spatial and expression communication data

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 : '/usr/bin/python3'
#>  python version : 3.10
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#>  "/usr/bin/python3"

exprCC <- exprCellCellcom(g,
    cluster_column = "leiden_clus",
    feat_set_1 = "Gm19935",
    feat_set_2 = "9630013A20Rik"
)

spatialCC <- spatCellCellcom(
    gobject = g,
    cluster_column = "leiden_clus",
    feat_set_1 = "Gm19935",
    feat_set_2 = "9630013A20Rik",
    verbose = "a lot",
    random_iter = 10
)
#> Error: package 'future' is not yet installed
#> 
#>  To install:
#> install.packages(c("future"))

combCC <- combCCcom(spatialCC = spatialCC, exprCC = exprCC)
#> Error: object 'spatialCC' not found
force(combCC)
#> Error: object 'combCC' not found