plotCCcomHeatmap: plotCCcomHeatmap

In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

plotCCcomHeatmap

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

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

RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.