Zoom on a Portion of a Phylogeny by Successive Clicks
This function plots simultaneously a whole phylogenetic tree (supposedly large) and a portion of it determined by clicking on the nodes of the phylogeny. On exit, returns the last subtree visualized.
subtreeplot(x, wait=FALSE, ...)
- an object of class
- a logical indicating whether the node beeing processed should be printed (useful for big phylogenies).
- further arguments passed to
This function aims at easily exploring very large trees. The main argument is a phylogenetic tree, and the second one is a logical indicating whether a waiting message should be printed while the calculation is being processed.
The whole tree is plotted on the left-hand side in half of the device. The subtree is plotted on the right-hand side in the other half. The user clicks on the nodes in the complete tree and the subtree corresponding to this node is ploted in the right-hand side. There is no limit for the number of clicks that can be done. On exit, the subtree on the right hand side is returned.
To use a subtree as the new tree in which to zoom, the user has to use the function many times. This can however be done in a single command line (see example 2).
#example 1: simple tree1 <- rtree(50) tree2 <- subtreeplot(tree1, wait = TRUE) # on exit, tree2 will be a subtree of tree1 #example 2: more than one zoom tree1 <- rtree(60) tree2 <- subtreeplot(subtreeplot(subtreeplot(tree1))) # allow three succssive zooms