plotRecovery: plotRecovery

In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

Description

Plots recovery plot to compare ligand-receptor rankings from spatial and expression information

Usage

plotRecovery(
  gobject,
  combCC,
  expr_rnk_column = "exprPI_rnk",
  spat_rnk_column = "spatPI_rnk",
  ground_truth = c("spatial", "expression"),
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "plotRecovery"
)

Arguments

gobject	giotto object
combCC	combined communinication scores from combCCcom
expr_rnk_column	column with expression rank information to use
spat_rnk_column	column with spatial rank information to use
ground_truth	what to consider as ground truth (default: spatial)
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

    plotRecovery(CPGscores)

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