ggalign (version 1.2.0)

fortify_data_frame.phylo: Build a data frame

Description

This function converts various objects to a data frame.

Usage

# S3 method for phylo
fortify_data_frame(
  data,
  ...,
  priority = "right",
  center = FALSE,
  type = "rectangle",
  tree_type = NULL,
  tip_pos = NULL,
  tip_clades = NULL,
  reorder_clades = TRUE,
  clade_gap = NULL,
  root = NULL,
  double = TRUE,
  data_arg = NULL,
  call = NULL
)

Value

A data frame with the node coordinates:

• .panel: Similar with panel column, but always give the correct panel for usage of the ggplot facet.

• .index: the original index in the tree for the the tip/node.

• label: the tip/node label text.

• x and y: x-axis and y-axis coordinates for the tip/node.

• clade: which clade the node is. You can use this column to color different clades.

• panel: which panel the node is, if we split the plot into panel using facet_grid, this column will show which panel the node is from. Note: some nodes may fall outside panel (between two panels), so there are possible NA values in this column.

• tip: A logical value indicates whether current node is a tip.

Arguments

data

A hclust or a dendrogram object.

...

These dots are for future extensions and must be empty.

priority

A string of "left" or "right". if we draw from right to left, the left will override the right, so we take the "left" as the priority. If we draw from left to right, the right will override the left, so we take the "right" as priority. This is used by align_dendro() to provide support of facet operation in ggplot2.

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".

tree_type

A single string, one of "phylogram" or "cladogram", indicating the type of tree.

• phylogram: Represents a phylogenetic tree where branch lengths indicate evolutionary distance or time.

• cladogram: Represents a tree where branch lengths are not used, or the branches do not reflect evolutionary time.

Usually, you don't need to modify this.

tip_pos

The x-coordinates of the tip. Must be the same length of the number of tips in tree.

tip_clades

Clades of the tips. Must be the same length of the number of tips in data.

reorder_clades

A single boolean value, indicates whether reorder the provided tip_clades based on the actual ordering index.

clade_gap

A single numeric value indicates the gap between different clades.

root

A length one string or numeric indicates the root branch.

double

A single logical value indicating whether horizontal lines should be doubled when segments span multiple branches. If TRUE, the horizontal lines will be repeated for each branch that the segment spans. If FALSE, only one horizontal line will be drawn. This is used by align_dendro() to provide support of facet operation in ggplot2.

data_arg

The argument name for data. Developers can use it to improve messages. Not used by the user.

call

The execution environment where data and other arguments for the method are collected. Developers can use it to improve messages. Not used by the user.

ggalign attributes

edge: A data frame for edge coordinates:

• .panel: Similar with panel column, but always give the correct panel for usage of the ggplot facet.

• x and y: x-axis and y-axis coordinates for the start node of the edge.

• xend and yend: the x-axis and y-axis coordinates of the terminal node for edge.

• clade: which panel the edge is. You can use this column to color different groups.

• panel1 and panel2: The panel1 and panel2 columns have the same functionality as panel, but they are specifically for the edge data and correspond to both nodes of each edge.

See Also

Other fortify_data_frame() methods: fortify_data_frame.GRanges(), fortify_data_frame.character(), fortify_data_frame.default(), fortify_data_frame.dendrogram(), fortify_data_frame.matrix()