plotCombineCCcom#

Last Updated: Sep 07, 2023

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#

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

Value#

ggplot