cellProximityHeatmap#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_interaction_visuals.R#L99

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#

Argument

Description

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_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 heatmap that shows the spatial proximity enrichment or depletion of cell type pairs.

Value#

ggplot heatmap