plotCombineICF

Create visualization for combined (pairwise) ICF scores

plotCombineICF(
  gobject,
  combIcfObject,
  selected_interactions = NULL,
  selected_feat_to_feat = NULL,
  detail_plot = TRUE,
  simple_plot = FALSE,
  simple_plot_facet = c("interaction", "feats"),
  facet_scales = "fixed",
  facet_ncol = length(selected_feat_to_feat),
  facet_nrow = length(selected_interactions),
  colors = c("#9932CC", "#FF8C00"),
  show_plot = NULL,
  return_plot = NULL,
  save_plot = NULL,
  save_param = list(),
  default_save_name = "plotCombineICF"
)

Arguments

gobject

giotto object

combIcfObject

ICFscores, output from combineInteractionChangedFeats()

selected_interactions

interactions to show

selected_feat_to_feat

pairwise feature combinations to show

detail_plot

show detailed info in both interacting cell types

simple_plot

show a simplified plot

simple_plot_facet

facet on interactions or feats with simple plot

facet_scales

ggplot facet scales paramter

facet_ncol

ggplot facet ncol parameter

facet_nrow

ggplot facet nrow parameter

colors

vector with two colors to use

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

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"

g_icf <- findInteractionChangedFeats(g,
    cluster_column = "leiden_clus",
    selected_feats = c("Gna12", "Ccnd2", "Btbd17"), nr_permutations = 10
)
#> Error: package 'future' is not yet installed
#> 
#>  To install:
#> install.packages(c("future"))

combIcfObject <- combineInteractionChangedFeats(g_icf)
#> Error: object 'g_icf' not found

plotCombineICF(
    gobject = g, combIcfObject = combIcfObject,
    selected_feat_to_feat = c("Btbd17--Ccnd2", "Btbd17--Gna12"),
    selected_interactions = "1--8"
)
#> Error: object 'combIcfObject' not found