cellProximityHeatmap: cellProximityHeatmap

In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

Description

Create heatmap from cell-cell proximity scores

Usage

cellProximityHeatmap(
  gobject,
  CPscore,
  scale = T,
  order_cell_types = T,
  color_breaks = NULL,
  color_names = NULL,
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "cellProximityHeatmap"
)

Arguments

gobject	giotto object
CPscore	CPscore, output from cellProximityEnrichment()
scale	scale cell-cell proximity interaction scores
order_cell_types	order cell types based on enrichment correlation
color_breaks	numerical vector of length 3 to represent min, mean and maximum
color_names	character color vector of length 3
show_plot	show plot
return_plot	return ggplot 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

Details

This function creates a heatmap that shows the spatial proximity enrichment or depletion of cell type pairs.

Value

ggplot heatmap

Examples

    cellProximityHeatmap(CPscore)

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