plotCCcomHeatmap#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_interaction_visuals.R#L2142

Description#

Plots heatmap for ligand-receptor communication scores in cell-cell interactions

Usage#

plotCCcomHeatmap(
  gobject,
  comScores,
  selected_LR = NULL,
  selected_cell_LR = NULL,
  show_LR_names = TRUE,
  show_cell_LR_names = TRUE,
  show = c("PI", "LR_expr", "log2fc"),
  cor_method = c("pearson", "kendall", "spearman"),
  aggl_method = c("ward.D", "ward.D2", "single", "complete", "average", "mcquitty",
    "median", "centroid"),
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "plotCCcomHeatmap"
)

Arguments#

Argument

Description

gobject

giotto object

comScores

communinication scores from `exp rCellCellcom <#exprcellcellcom>`__ or `spa tCellCellcom <#spatcellcellcom>`__

selected_LR

selected ligand-receptor combinations

selected_cell_LR

selected cell-cell combinations for ligand-receptor combinations

show_LR_names

show ligand-receptor names

show_cell_LR_names

show cell-cell names

show

values to show on heatmap

cor_method

correlation method used for clustering

aggl_method

agglomeration method used by hclust

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