Man pages for gjuggler/ggphylo
Tools for laying out and plotting phylogenetic data (trees and alignments) with ggplot.

as.character.phyloTurns a phylo object into a Newick format string...
as.data.frame.phyloTurns a phylo object into a data frame
checkLabelChecks a tree for a valid label, optionally removing bad...
clado.buildInternal function, taken directly from 'ape'.
geom_joinedsegmentCreate the function for geom_joinedsegment
GeomJoinedSegmentCreate a geom_joinedsegment which joins together segments...
ggphyloPlots a tree or a list of trees using 'ggplot'.
is.leaf.phyloDetermine if the given node is a leaf or an internal node....
is.treeReturns TRUE if the given object appears to be a valid tree...
label.phyloReturns the label for the given node. Alias for...
labels.phyloReturns labels corresponding to all or some subset of the...
leavesReturns a vector of node indices for all the leaves in the...
nodesReturns a vector of node indices for all nodes (leaves plus...
order.nodes.visuallyReturns the indices of all nodes in the tree, arranged in the...
sort.df.by.treeSorts a data frame according to a tree. Requires the data...
tags.into.dfGiven a 'phylo' object and a data frame, transform all the...
tags.phyloRetrieves a list of all tags for the given node. Convenience...
tags.to.nhx.stringConverts a list of tags to an NHX annotation string.
theme_phylo_blackA white-on-black theme for futuristic plots.
theme_phylo_blankA mostly-blank theme for simple plots. Ruthlessly taken from...
tree.apply.branchlengthsRemoves branch lengths from a tree
tree.as.data.frameCreate a data frame from a phylo object where each row...
tree.branch.lengthExtracts the length of the branch above the given node....
tree.child.nodesReturn a list (not a vector!) of the node indices of the...
tree.depth.to.rootReturns the length from the tree root to the given node....
tree.extract.cladeReturns the sub-tree beneath the given node.
tree.extract.subtreeReturns the minimum sub-tree connecting the given leaf nodes
tree.findReturns the index of the node with a given label. Alias for...
tree.foreachLoops over nodes in the tree, applying a function using each...
tree.get.labelReturns the label for a given node in the tree. Alias for...
tree.get.rootReturns the index of the root node in the tree, or NA if...
tree.get.tagRetrieves a named tag from the given node. Tags are usually...
tree.get.tagsRetrieves a list of all tags for the given node.
tree.has.tagsDetermines whether the given phylo object contains tags or...
tree.is.leafDetermine if the given node is a leaf or an internal node.
tree.label.for.nodeReturns the label for a given node in the tree.
tree.layoutReturns a data frame defining segments to draw the...
tree.leaves.beneathReturns the number of leaves beneath a node in the tree...
tree.lengths.to.rootReturns a vector containing the root-to-tip branch length for...
tree.length.to.rootReturns the length from the tree root to the given node. The...
tree.load.dataLoads a data.frame or CSV file into a tree as tags. Requires...
tree.max.length.to.rootReturns the maximum root-to-tip branch length in the tree....
tree.mean.path.lengthReturns the mean root-to-tip path length of the tree. This is...
tree.node.with.labelReturns the index of the node with a given label.
tree.normalize.branchlengthsNormalizes the branch lengths of a tree for cleaner...
tree.parent.nodeExtracts the parent node index for the given node. Returns -1...
tree.readReads a tree and returns a phylo object. Note: this function...
tree.read.nhxReads a tree annotated with NHX-formatted annotations. A...
tree.remove.leafRemoves a single leaf from the tree and returns a copy.
tree.remove.node.labelsRemoves internal node labels from a tree
tree.scale.byScales the tree by a given multiplicative factor.
tree.scale.toScales the tree to a given total branch length.
tree.set.labelReplaces the label of a given node and returns a new phylo...
tree.set.tagSets the tag for a given node to the specified value. Returns...
tree.strip.branchlengthsRemoves branch lengths from a tree
tree.tags.to.labelsConverts all tags from a tree into NHX annotations and...
tree.to.stringConverts a phylo object into a Newick-format string...
tree.total.branch.lengthReturns the total branch length of the tree
tree.translateTranslates all labels in the tree based on a list of label...
write.nhxWrites the phylo object to disk in NHX format.
gjuggler/ggphylo documentation built on May 14, 2017, 12:06 p.m.