treeFun-package: Functions for dealing with genetic data

In cbaumbach/treeFun: Functions for dealing with tree structures

Description

This is a collection of functions for creating, manipulation, and plotting tree structures. If you want to convert your trees into displayable file formats, you will need the open source graph visualization software Graphviz (www.graphviz.org).

Details

Package:	treeFun
Type:	Package
Version:	1.0
Date:	2015-03-17
License:	GPL (>= 2)

Index:

  edges         Extract edges of tree object
  extract_tree  Downstream extraction of subtrees
  induced_tree  Build tree induced by set of node ids
  make_tree     Convert data frame to tree structure
  nodes         Extract nodes of tree object
  overlap_tree  Find common subtree
  tree_equal    Test if two trees have the same edges
  tree2dot      Write tree to dot file

Author(s)

Clemens Baumbach

Maintainer: Clemens Baumbach <[e-mail]>

References

Graphviz (open source graph visualization software, www.graphviz.org).

See Also

tree2dot

Examples

library(treeFun)

d <- read.table(textConnection("\
id parents label
0 - a
1 0 b
2 0 c
3 1 d
4 1 e
5 1 f
6 2 g
7 2 h
8 7 i
"), header = TRUE, stringsAsFactors = FALSE)

##         0a
##        / \
##      /     \
##    1b       2c
##   /|\      / \
##  / | \    /   \
## 3d 4e 5f 6g    7h
##                 \
##                  \
##                   8i

rownames(d) <- d$id

d2 <- d
d2$label <- toupper(d$label)
d2 <- d2[sample.int(nrow(d2)),]

## d2 has the same structure as d1 but its labels are in uppercase and
## its rows are permuted.

tr <- make_tree(d)
tr2 <- make_tree(d2)

tree_equal(tr, tr2)

stopifnot(tree_equal(extract_tree(tr, 999), tr))
stopifnot(tree_equal(extract_tree(tr, 2, from = 1), make_tree(d[c("1", "3", "4", "5"), ])))

nodes(tr)
edges(tr)

## Not run: tree2dot(tr, "tree.dot")

itr1 <- induced_tree(c("1","8"), tr)
itr2 <- induced_tree(c("2","5"), tr)

overlap_tree(list(itr1, itr2))

cbaumbach/treeFun documentation built on May 13, 2019, 1:49 p.m.