plot_tree: Plot MRtree results as hierarchical cluster tree.

In pengminshi/MRtree: Multi-resolution Reconciled Tree

Plot MRtree results as hierarchical cluster tree.

Description

Plot MRtree results as a dendrogram. If reference labels are provided, a pie chart is shown at each tree node, giving the label proprotions for respective cluster.

Usage

plot_tree(
  labelmat,
  ref.labels = NULL,
  show.ref.labels = TRUE,
  label.order = NULL,
  node.size = 0.2,
  cols = NULL,
  plot.piechart = TRUE,
  tip.labels = NULL,
  tip.label.dist = 4,
  show.branch.labels = FALSE,
  branch.label.dist = 10,
  flip.branch = NULL,
  legend.title = "",
  bottom.margin = 25
)

Arguments

labelmat	a n by m label matrix, provided by the ouput of mrtree function, labelmat.mrtree
ref.labels	a factor or characteristic vector specifying the reference labels of n data points
show.ref.labels	boolean, whether to show the labels of major type at tree nodes and tips
label.order	a vector specifying the order of labels for default colors
node.size	scalar, the size of the pie chart / node
cols	a vector of colors, one per each label. If not provided, use the default colors.
plot.piechart	boolean, whether to draw the pie chart for each tree node.
tip.labels	a vector of strings specifying the labels of tree leafs. The labels should align with the order of leaf in the plot.
tip.label.dist	vertical distance of the tip labels to the tree tips
show.branch.labels	boolean, whether to show the branch labels for convenience of flipping branches
branch.label.dist	vertical distance from branch node labels to the node
flip.branch	a list of vectors each of size 2, indicating the branch labels to flip. Each time two branches are flipped.
legend.title	string as legend title. Empty string by default.
bottom.margin	size of the bottom margin, need to be adjusted to show the full labels.

Examples

data("clust_example")
out = mrtree(clust_example$clusterings)
plot_tree(labelmat = out$labelmat.mrtree, ref.labels = clust_example$ref.labels, plot.piechart = TRUE)

pengminshi/MRtree documentation built on March 6, 2023, 4:20 p.m.