plotCombineCellProximityGenes: plotCombineCellProximityGenes

In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

Description

Create visualization for combined (pairwise) cell proximity gene scores

Usage

plotCombineCellProximityGenes(
  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 = "plotCombineCPG"
)

Arguments

gobject	giotto object
combCpgObject	CPGscores, output from combineCellProximityGenes()
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

Examples

    plotCombineCellProximityGenes(CPGscores)

bernard2012/Giotto documentation built on Sept. 22, 2020, 10:29 a.m.