plotCombineInteractionChangedGenes

Create visualization for combined (pairwise) ICG scores

plotCombineInteractionChangedGenes(
  gobject,
  combCpgObject,
  selected_interactions = NULL,
  selected_gene_to_gene = NULL,
  detail_plot = T,
  simple_plot = F,
  simple_plot_facet = c("interaction", "genes"),
  facet_scales = "fixed",
  facet_ncol = length(selected_gene_to_gene),
  facet_nrow = length(selected_interactions),
  colors = c("#9932CC", "#FF8C00"),
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "plotCombineICG"
)

Arguments

gobject

giotto object

combCpgObject

ICGscores, output from combineInteractionChangedGenes()

selected_interactions

interactions to show

selected_gene_to_gene

pairwise gene 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 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_function

default_save_name

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

Value

ggplot