ggalign (version 1.0.1)

align_dendro: Plot dendrogram tree

Description

Plot dendrogram tree

Usage

align_dendro(
  mapping = aes(),
  ...,
  distance = "euclidean",
  method = "complete",
  use_missing = "pairwise.complete.obs",
  reorder_dendrogram = FALSE,
  merge_dendrogram = FALSE,
  reorder_group = FALSE,
  k = NULL,
  h = NULL,
  cutree = NULL,
  plot_dendrogram = TRUE,
  plot_cut_height = NULL,
  root = NULL,
  center = FALSE,
  type = "rectangle",
  size = NULL,
  data = NULL,
  no_axes = NULL,
  active = NULL
)

Arguments

mapping

Default list of aesthetic mappings to use for plot. If not specified, must be supplied in each layer added to the plot.

...

<dyn-dots> Additional arguments passed to geom_segment().

distance

A string of distance measure to be used. This must be one of "euclidean", "maximum", "manhattan", "canberra", "binary" or "minkowski". Correlation coefficient can be also used, including "pearson", "spearman" or "kendall". In this way, 1 - cor will be used as the distance. In addition, you can also provide a dist object directly or a function return a dist object. Use NULL, if you don't want to calculate the distance.

method

A string of the agglomeration method to be used. This should be (an unambiguous abbreviation of) one of "ward.D", "ward.D2", "single", "complete", "average" (= UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid" (= UPGMC). You can also provide a function which accepts the calculated distance (or the input matrix if distance is NULL) and returns a hclust object. Alternative, you can supply an object which can be coerced to hclust.

use_missing

An optional character string giving a method for computing covariances in the presence of missing values. This must be (an abbreviation of) one of the strings "everything", "all.obs", "complete.obs", "na.or.complete", or "pairwise.complete.obs". Only used when distance is a correlation coefficient string.

reorder_dendrogram

A single boolean value indicating whether to reorder the dendrogram based on the means. Alternatively, you can provide a custom function that accepts an hclust object and the data used to generate the tree, returning either an hclust or dendrogram object. Default is FALSE.

merge_dendrogram

A single boolean value, indicates whether we should merge multiple dendrograms, only used when previous groups have been established. Default: FALSE.

reorder_group

A single boolean value, indicates whether we should do Hierarchical Clustering between groups, only used when previous groups have been established. Default: FALSE.

k

An integer scalar indicates the desired number of groups.

h

A numeric scalar indicates heights where the tree should be cut.

cutree

A function used to cut the hclust tree. It should accept four arguments: the hclust tree object, distance (only applicable when method is a string or a function for performing hierarchical clustering), k (the number of clusters), and h (the height at which to cut the tree). By default, cutree() is used.

plot_dendrogram

A boolean value indicates whether plot the dendrogram tree.

plot_cut_height

A boolean value indicates whether plot the cut height.

root

A length one string or numeric indicates the root branch.

center

A boolean value. if TRUE, nodes are plotted centered with respect to all leaves/tips in the branch. Otherwise (default), plot them in the middle of the direct child nodes.

type

A string indicates the plot type, "rectangle" or "triangle".

size

The relative size of the plot, can be specified as a unit(). Note that for circle_layout(), all size values will be interpreted as relative sizes, as this layout type adjusts based on the available space in the circular arrangement.

data

A matrix-like object. By default, it inherits from the layout matrix.

no_axes

Logical; if TRUE, removes axes elements for the alignment axis using theme_no_axes(). By default, will use the option- "ggalign.align_no_axes".

active

A active() object that defines the context settings when added to a layout.

ggplot2 specification

align_dendro initializes a ggplot data and mapping.

The internal ggplot object will always use a default mapping of aes(x = .data$x, y = .data$y).

The default ggplot data is the node coordinates with edge data attached in ggalign attribute, in addition, a geom_segment layer with a data frame of the edge coordinates will be added when plot_dendrogram = TRUE.

See fortify_data_frame.dendrogram() for details.

Discrete Axis Alignment

It is important to note that we consider rows as observations, meaning vec_size(data)/NROW(data) must match the number of observations along the axis used for alignment (x-axis for a vertical stack layout, y-axis for a horizontal stack layout).

Examples

# align_dendro will always add a plot area
ggheatmap(matrix(rnorm(81), nrow = 9)) +
    anno_top() +
    align_dendro()
ggheatmap(matrix(rnorm(81), nrow = 9)) +
    anno_top() +
    align_dendro(k = 3L)