Combine a phylogenetic tree with a locus coverage heatmap

This script uses R to combine a presence absence matrix (1/0), and a NEWICK formated phylogenetic tree to generate a heatmap plotted against the tree.

Typically, I've used this for examining coverage of UCE loci / target enrichment coverage by taxon. It can be used for anything that has a presence/absence matrix and a tree.

For the example, I've pulled data from the Phyluce pipeline, after the match_contigs_to_probe script step.

To get a presence/absence matrix from SQLite database file generated by script:

sqlite3 probe3.matches.sqlite
.mode columns
.mode csv
.headers on
.nullvalue 0
.output matches_uce.csv
SELECT * FROM matches;
.exit

Tree_Heatmap.r

This script will generate a file that looks like this:

Inputs are:

1. 1/0 presence absence matrix.
2. Newik formatted tree file.

Adjust file names in the script as needed.

Note: R is smart enough to still plot the tree even if the matrix is missing taxa. The missing taxa just wont show up on the plot.

Limitations:

This can only generate a dendrogram style tree, so branch lengths are lost.

Missing_Plot.r

This was a first attempt at the problem. It will generate a heatmap, which is useful if you need to order the heatmap by presence etc., but does not include the option to add a tree.

It will generate plots like this:

Input is:

1. 1/0 presence absence matrix.

Adjust file name in the script as needed.