cellProximityBarplot: cellProximityBarplot

In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

Description

Create barplot from cell-cell proximity scores

Usage

cellProximityBarplot(
  gobject,
  CPscore,
  min_orig_ints = 5,
  min_sim_ints = 5,
  p_val = 0.05,
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "cellProximityBarplot"
)

Arguments

gobject	giotto object
CPscore	CPscore, output from cellProximityEnrichment()
min_orig_ints	filter on minimum original cell-cell interactions
min_sim_ints	filter on minimum simulated cell-cell interactions
p_val	p-value
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 barplot that shows the spatial proximity enrichment or depletion of cell type pairs.

Value

ggplot barplot

Examples

    cellProximityBarplot(CPscore)

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