raman-taxonomy

This repository contains analysis code to accompany the publication 'Identifying the phylogenetic utility of Raman spectra'.

Notebooks containing expanded methods and the code + analyses for generating all figures in the publication can be found in this Jupyter notebook.

This repository uses conda to manage software environments and installations. You can find operating system-specific instructions for installing miniconda here. After installing conda and mamba, run the following command to create the run environment.

mamba env create --file environment.yml
mamba activate raman-taxonomy

Following this, you can run the Jupyter notebook as usual.

Note: The conda environment has been tested with a Mac OSX running the Intel x64 architecture. While most packages should be available on Linux distributions, not all packages are available on the new Apple M1/M2 ARM64 architecture.

Directory structure

00_data/ Raman spectra and associated metadata.
01_notebooks/ Jupyter notebooks outlining the full suite of analyses presented in the pub.
02_outputs/ Outputs associated with the pub.

Data

Raman spectra data from Ho et al. 2019 were acquired from the link provided with the original publication. The taxonomic breadth and sample sizes (n=100/strain) led us to decide on using this dataset for these exploratory analyses.

Taxonomic classifications were obtained by searching for each species on the NCBI Taxonomy Database.

The time-calibrated tree was downloaded from timetree.org by querying species names.

R packages and versions used in this repo:

TreeDist v2.6.0
ArcadiaColorBrewer@c6cea41
scales v1.2.1
phytools v1.2-0
ape v3.4.1
lsa v0.73.3
plotrix v3.8-2
reticulate v1.27
here v1.0.1