filterInteractionChangedFeats

Filter Interaction Changed Feature scores.

filterInteractionChangedFeats(
  icfObject,
  min_cells = 4,
  min_cells_expr = 1,
  min_int_cells = 4,
  min_int_cells_expr = 1,
  min_fdr = 0.1,
  min_spat_diff = 0.2,
  min_log2_fc = 0.2,
  min_zscore = 2,
  zscores_column = c("cell_type", "feats"),
  direction = c("both", "up", "down")
)

filterICF(
  icfObject,
  min_cells = 4,
  min_cells_expr = 1,
  min_int_cells = 4,
  min_int_cells_expr = 1,
  min_fdr = 0.1,
  min_spat_diff = 0.2,
  min_log2_fc = 0.2,
  min_zscore = 2,
  zscores_column = c("cell_type", "feats"),
  direction = c("both", "up", "down")
)

Arguments

icfObject

ICF (interaction changed feature) score object

min_cells

minimum number of source cell type

min_cells_expr

minimum expression level for source cell type

min_int_cells

minimum number of interacting neighbor cell type

min_int_cells_expr

minimum expression level for interacting neighbor cell type

min_fdr

minimum adjusted p-value

min_spat_diff

minimum absolute spatial expression difference

min_log2_fc

minimum log2 fold-change

min_zscore

minimum z-score change

zscores_column

calculate z-scores over cell types or genes

direction

differential expression directions to keep

Value

icfObject that contains the filtered differential feature scores

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

icf <- findInteractionChangedFeats(g,
     cluster_column = "leiden_clus",
     selected_feats = c("Gna12", "Ccnd2", "Btbd17"),
     nr_permutations = 10
)
#> Error in loadNamespace(x): there is no package called ‘future.apply’
force(icf)
#> Error in eval(expr, envir, enclos): object 'icf' not found
force(icf$ICFscores)
#> Error in eval(expr, envir, enclos): object 'icf' not found

icf_filter1 <- filterInteractionChangedFeats(icf, min_cells = 4)
#> Error in eval(expr, envir, enclos): object 'icf' not found
force(icf_filter1)
#> Error in eval(expr, envir, enclos): object 'icf_filter1' not found
force(icf_filter1$ICFscores)
#> Error in eval(expr, envir, enclos): object 'icf_filter1' not found

# filterICF is a simple alias with a shortened name
icf_filter2 <- filterICF(icf, min_cells = 4)
#> Error in eval(expr, envir, enclos): object 'icf' not found
force(icf_filter2)
#> Error in eval(expr, envir, enclos): object 'icf_filter2' not found