cellProximityBarplot

Create barplot from cell-cell proximity scores

cellProximityBarplot(
  gobject,
  CPscore,
  min_orig_ints = 5,
  min_sim_ints = 5,
  p_val = 0.05,
  show_plot = NULL,
  return_plot = NULL,
  save_plot = NULL,
  save_param = list(),
  default_save_name = "cellProximityBarplot"
)

Arguments

gobject

giotto object

CPscore

CPscore, output from cellProximityEnrichment()

min_orig_ints

filter on minimum original cell-cell interactions

min_sim_ints

filter on minimum simulated cell-cell interactions

p_val

p-value

show_plot

logical. show plot

return_plot

logical. return ggplot object

save_plot

logical. save the plot

save_param

list of saving parameters, see showSaveParameters

default_save_name

default save name for saving, don't change, change save_name in save_param

Value

ggplot barplot

Details

This function creates a barplot that shows the spatial proximity enrichment or depletion of cell type pairs.

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"

cellProximityBarplot(
    gobject = g,
    CPscore = cellProximityEnrichment(g, cluster_column = "leiden_clus")
)