Man pages for gjuggler/ggphylo
Tools for laying out and plotting phylogenetic data (trees and alignments) with ggplot.
| as.character.phylo | Turns a phylo object into a Newick format string... |
| as.data.frame.phylo | Turns a phylo object into a data frame |
| checkLabel | Checks a tree for a valid label, optionally removing bad... |
| clado.build | Internal function, taken directly from 'ape'. |
| geom_joinedsegment | Create the function for geom_joinedsegment |
| GeomJoinedSegment | Create a geom_joinedsegment which joins together segments... |
| ggphylo | Plots a tree or a list of trees using 'ggplot'. |
| is.leaf.phylo | Determine if the given node is a leaf or an internal node.... |
| is.tree | Returns TRUE if the given object appears to be a valid tree... |
| label.phylo | Returns the label for the given node. Alias for... |
| labels.phylo | Returns labels corresponding to all or some subset of the... |
| leaves | Returns a vector of node indices for all the leaves in the... |
| nodes | Returns a vector of node indices for all nodes (leaves plus... |
| order.nodes.visually | Returns the indices of all nodes in the tree, arranged in the... |
| sort.df.by.tree | Sorts a data frame according to a tree. Requires the data... |
| tags.into.df | Given a 'phylo' object and a data frame, transform all the... |
| tags.phylo | Retrieves a list of all tags for the given node. Convenience... |
| tags.to.nhx.string | Converts a list of tags to an NHX annotation string. |
| theme_phylo_black | A white-on-black theme for futuristic plots. |
| theme_phylo_blank | A mostly-blank theme for simple plots. Ruthlessly taken from... |
| tree.apply.branchlengths | Removes branch lengths from a tree |
| tree.as.data.frame | Create a data frame from a phylo object where each row... |
| tree.branch.length | Extracts the length of the branch above the given node.... |
| tree.child.nodes | Return a list (not a vector!) of the node indices of the... |
| tree.depth.to.root | Returns the length from the tree root to the given node.... |
| tree.extract.clade | Returns the sub-tree beneath the given node. |
| tree.extract.subtree | Returns the minimum sub-tree connecting the given leaf nodes |
| tree.find | Returns the index of the node with a given label. Alias for... |
| tree.foreach | Loops over nodes in the tree, applying a function using each... |
| tree.get.label | Returns the label for a given node in the tree. Alias for... |
| tree.get.root | Returns the index of the root node in the tree, or NA if... |
| tree.get.tag | Retrieves a named tag from the given node. Tags are usually... |
| tree.get.tags | Retrieves a list of all tags for the given node. |
| tree.has.tags | Determines whether the given phylo object contains tags or... |
| tree.is.leaf | Determine if the given node is a leaf or an internal node. |
| tree.label.for.node | Returns the label for a given node in the tree. |
| tree.layout | Returns a data frame defining segments to draw the... |
| tree.leaves.beneath | Returns the number of leaves beneath a node in the tree... |
| tree.lengths.to.root | Returns a vector containing the root-to-tip branch length for... |
| tree.length.to.root | Returns the length from the tree root to the given node. The... |
| tree.load.data | Loads a data.frame or CSV file into a tree as tags. Requires... |
| tree.max.length.to.root | Returns the maximum root-to-tip branch length in the tree.... |
| tree.mean.path.length | Returns the mean root-to-tip path length of the tree. This is... |
| tree.node.with.label | Returns the index of the node with a given label. |
| tree.normalize.branchlengths | Normalizes the branch lengths of a tree for cleaner... |
| tree.parent.node | Extracts the parent node index for the given node. Returns -1... |
| tree.read | Reads a tree and returns a phylo object. Note: this function... |
| tree.read.nhx | Reads a tree annotated with NHX-formatted annotations. A... |
| tree.remove.leaf | Removes a single leaf from the tree and returns a copy. |
| tree.remove.node.labels | Removes internal node labels from a tree |
| tree.scale.by | Scales the tree by a given multiplicative factor. |
| tree.scale.to | Scales the tree to a given total branch length. |
| tree.set.label | Replaces the label of a given node and returns a new phylo... |
| tree.set.tag | Sets the tag for a given node to the specified value. Returns... |
| tree.strip.branchlengths | Removes branch lengths from a tree |
| tree.tags.to.labels | Converts all tags from a tree into NHX annotations and... |
| tree.to.string | Converts a phylo object into a Newick-format string... |
| tree.total.branch.length | Returns the total branch length of the tree |
| tree.translate | Translates all labels in the tree based on a list of label... |
| write.nhx | Writes the phylo object to disk in NHX format. |
