plotCombineCellCellCommunication

Create visualization for combined (pairwise) cell proximity gene scores

plotCombineCellCellCommunication(
  gobject,
  combCCcom,
  selected_LR = NULL,
  selected_cell_LR = NULL,
  detail_plot = TRUE,
  simple_plot = FALSE,
  simple_plot_facet = c("interaction", "genes"),
  facet_scales = "fixed",
  facet_ncol = length(selected_LR),
  facet_nrow = length(selected_cell_LR),
  colors = c("#9932CC", "#FF8C00"),
  show_plot = NULL,
  return_plot = NULL,
  save_plot = NULL,
  save_param = list(),
  default_save_name = "plotCombineCellCellCommunication"
)

Arguments

gobject

giotto object

combCCcom

combined communcation scores, output from combCCcom()

selected_LR

selected ligand-receptor pair

selected_cell_LR

selected cell-cell interaction pair for ligand-receptor pair

detail_plot

show detailed info in both interacting cell types

simple_plot

show a simplified plot

simple_plot_facet

facet on interactions or genes 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"

comScores <- exprCellCellcom(g,
    cluster_column = "leiden_clus",
    feat_set_1 = c("Gm19935", "2900040C04Rik", "Ccnd2"),
    feat_set_2 = c("9630013A20Rik", "Gna12", "Btbd17")
)

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"
)
#> Error: package 'future' is not yet installed
#> 
#>  To install:
#> install.packages(c("future"))

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

plotCombineCellCellCommunication(
    gobject = g, combCCcom = combCCcom,
    selected_LR = c("Gm19935-9630013A20Rik"), selected_cell_LR = c("1--1")
)
#> Error in combCCcom[LR_comb %in% selected_LR & LR_cell_comb %in% selected_cell_LR]: object of type 'closure' is not subsettable