filterICF — filterICF • Giotto

Filter Interaction Changed Feature scores.

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 features
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
#> cell_spatInfo_spatVector.shp
#> cell
#> 
#> 3.2 read Giotto spatial centroid information
#> cell
#> 
#> 3.3 read Giotto spatial overlap information
#> No overlaps were found, overlap loading will be
#>  skipped
#> 
#> 4. read Giotto image information
#> a giotto python environment was found
#> Using python path:
#>  "/Users/yuanlab/Library/r-miniconda/envs/giotto_env/bin/pythonw"

g_icf <- findInteractionChangedFeats(g, cluster_column = "leiden_clus")

filterICF(g_icf)
#> An object of class icfObject 
#>  -dimensions : 84, 21 (icfs, attributes)
#> <giotto info>
#>  -values          : normalized
#>  -cluster         : leiden_clus
#>  -spatial network : Delaunay_network
#> <test info>
#>  -test                   : permutation
#>  -p.adj                  : bonferroni
#>  -min cells              : 1
#>  -min interacting cells  : 1
#>  -exclude selected cells : TRUE
#>  -perm                   : 1000