Plot Ligand-Receptor Communication Scores

plotCCcomDotplot()

Plots dotplot for ligand-receptor communication scores in cell-cell interactions.

plotCCcomDotplot(
    gobject,
    comScores,
    selected_LR = NULL,
    selected_cell_LR = NULL,
    show_LR_names = TRUE,
    show_cell_LR_names = TRUE,
    cluster_on = 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 = "plotCCcomDotplot"
)

Arguments

gobject	giotto object
comScores	communication 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
cluster_on	values to use for clustering of cell-cell and ligand-receptor pairs
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

A ggplot.