Bio.Phylogeny.PhyBin.Visualize

Documentation

dotNewickTree :: String -> Double -> FullTree StandardDecor -> DotGraph Node

Convert a NewickTree to a graphviz Dot graph representation.

dotToPDF :: DotGraph Node -> FilePath -> IO (Maybe FilePath)

Convert a .dot file to .pdf.

viewNewickTree :: String -> FullTree StandardDecor -> IO (Chan (), FullTree StandardDecor)

Open a GUI window to displaya tree.

Fork a thread that then runs graphviz. The channel retuned will carry a single message to signal completion of the subprocess.

dotNewickTree_debug :: String -> FullTree StandardDecor -> DotGraph Node

This version shows the ordered/rooted structure of the normalized tree.

Dendrogram visualization

dendrogramToGraph :: Int -> Dendrogram (FullTree a) -> DendroGraph

Create a graph using TreeNames for node labels and edit-distance for edge labels.

dotDendrogram :: PhyBinConfig -> String -> Double -> Dendrogram (FullTree a) -> Maybe (Map TreeName Int) -> [[NewickTree ()]] -> DotGraph Node

Convert to a dotGraph. Some duplicated code with dotNewickTree.