cellProximityBarplot#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_interaction_visuals.R#L20

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#

Argument

Description

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_f unction <#allplotssavefunction>`__

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