plotCCcomHeatmap

Source: R/spatial_interaction_visuals.R

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

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

gobject

giotto object
comScores

communinication scores from exprCellCellcom or 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_function
default_save_name

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

Value

ggplot