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.
Bubble tree is written with python 3+ and relies on the following packages:
pip install bubbletree
conda install -c aemann01 bubbletree
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