Create Cluster Dendrogram

showClusterDendrogram()

Creates dendrogram for selected clusters.

showClusterDendrogram(
    gobject,
    expression_values = c("normalized", "scaled", "custom"),
    cluster_column,
    cor = c("pearson", "spearman"),
    distance = "ward.D",
    h = NULL,
    h_color = "red",
    rotate = FALSE,
    show_plot = NA,
    return_plot = NA,
    save_plot = NA,
    save_param = list(),
    default_save_name = "showClusterDendrogram",
    ...
)

Arguments

gobject	giotto object
expression_values	expression values to use
cluster_column	name of column to use for clusters
cor	correlation score to calculate distance
distance	distance method to use for hierarchical clustering
h	height of horizontal lines to plot
h_color	color of horizontal lines
rotate	rotate dendrogram 90 degrees
show_plot	show plot
return_plot	return ggplot object
save_plot	directly save the plot [boolean]
save_param	list of saving parameters, see showSaveParameters
default_save_name	default save name for saving, don’t change, change save_name in save_param
…	additional parameters for ggdendrogram()

Value

A ggplot value.

Details

Expression correlation dendrogram for selected clusters.

Examples

data(mini_giotto_single_cell)

# cell metadata
cell_metadata = pDataDT(mini_giotto_single_cell)

# create heatmap
showClusterDendrogram(mini_giotto_single_cell,
          cluster_column = 'cell_types')