plotCombineCCcom#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_interaction_visuals.R#L2084

Description#

Create visualization for combined (pairwise) cell proximity gene scores

Usage#

plotCombineCCcom(
  gobject,
  combCCcom,
  selected_LR = NULL,
  selected_cell_LR = NULL,
  detail_plot = T,
  simple_plot = F,
  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 = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "plotCombineCCcom"
)

Arguments#

Argument

Description

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

show plots

return_plot

return plotting object

save_plot

directly save the plot [boolean]

save_param

list of saving parameters from `all_plots_save_f unction <#allplotssavefunction>`__

default_save_name

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

Value#

ggplot