showClusterDendrogram — showClusterDendrogram • Giotto

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

ggplot

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')