thebustalab / phylochemistry

R code phylochemistry

phylochemistry: integated analyses of chemical and sequence data in the context of phylogeny

phylochemistry is a set of functions for chemical and genomic/transcriptomic analysis. These tools are provided though a combination of new functions and wrapped features of previously developed packages. A number of new functions to streamline analyses in this interdisciplinary space are also provided. This repository contains the latest version of the phylochemistry R package.

INSTALL

phylochemistry can be installed by following these four steps:

1. Install msa and phangorn by running the following code in R

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("msa")
BiocManager::install("ggtree")
BiocManager::install("phangorn")
BiocManager::install("seqinr")
BiocManager::install("Biostrings")
BiocManager::install("GenomicRanges")

2. Install prequisite R packages by running the following code in R

install.packages("devtools")
install.packages("tidyverse")
install.packages("DT")
install.packages("RColorBrewer")
install.packages("xcms")
install.packages("data.table")
install.packages("rhandsontable")
install.packages("ape")
install.packages("ips")

3. (for Windows only) install RTools

4. (for Mac only) install XCode via the Mac AppStore

5. Restart R and install phylochemistry

devtools::install_github("thebustalab/phylochemistry", quiet = FALSE, force = TRUE)
library(phylochemistry)

VIGNETTE

The phylochemistry package is documented in this vignette.

NEW FEATURES

1. A Shiny app for GC-FID and GC-MS data analysis.
2. Open reading frame extraction from multiple fasta files.
3. Store BLAST results in a .csv file.
4. Minor ticks for ggplot2 axes.
5. Phylogenetic signal for discrete traits.
6. Analyze multiple sequence alignments for sites associated with user-defined function
7. Multiple column name, multiple row name data structures (aka "polylists").
8. Draw annotated multiple sequence alignments.
9. Use image analysis to automatically get the csv of a mass spectrum from a published image.
10. Draw chemical structures in R from a csv of molecular coordinates.

WRAPPED FEATURES

1. BLAST transcriptomes, via NCBI BLAST+.
2. Multiple sequence alignments and codon alignments of amino acid and nucleotide sequences, via msa and orthologr.
3. Phylogenetic tree construction (including g-blocks trimming, pruning, ancestral states reconstruction), via phangorn.
4. Systematic read/write functions (csv, newick, wide tables, fasta, summary statistic tables, GFFs, chromatograms, mass spectra).
5. Phylogenetic signal for continuous traits.