plotRecovery#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_interaction_visuals.R#L2543

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#

Argument

Description

gobject

giotto object

combCC

combined communinication scores from `combCCcom <#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_f unction <#allplotssavefunction>`__

default_save_name

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

Value#

ggplot