Bubble Tree

BubbleTree generates a Cleveland dot plot or heatmap ordered by a corresponding phylogenetic tree. Required input: a tab separated frequency table (i.e., with taxa as rows and samples as columns), a newick, nexus, nexml, phyloxml, or cdao formated tree, and a tab separated file with sample metdata. See example files for formatting requirements.

Prerequisites

Bubble tree is written with python 3+ and relies on the following packages:

• BioPython
• Matplotlib
• Pandas
• Numpy
• Seaborn

Install with pip

pip install bubbletree

Install with conda

conda install -c aemann01 bubbletree

Examples

Generate a heatmap figure ordered by the mapping.txt column Habitat2

bubbletree.py -i examples/biom.txt -t examples/tree.tre -m examples/map.txt -c Habitat2 -d heatmap -s sampleID -a ASVID

Generate a bubble chart figure colored and ordered by the mapping.txt column Species and view the tree structure in ASCII format to screen

bubbletree.py -i examples/biom.txt -t examples/tree.tre -m examples/map.txt -c Species -d bubblechart -p True -s sampleID -a ASVID

Generate a bubble chart figure colored and ordered by the mapping.txt column Genus on a remote cluster (Disables the automatic $DISPLAY environment varible used by matplotlib)

bubbletree.py -i examples/biom.txt -t examples/tree.tre -m examples/map.txt -c Genus -d bubblechart -r True -s sampleID -a ASVID

Help and parameter description

bubbletree.py -h