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Everything needed to perform self-organizing map clustering using the Catharanthus roseus transcriptome
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README.md
c.roseus.transcriptome.csv
implicated_genes.csv
som.R

README.md

Catharanthus roseus self-organizing map clustering

The files in this repository recreate figure 2 from the paper "An NPF transporter exports a central monoterpene indole alkaloid intermediate from the vacuole".

The transcriptome data is the same as that available from the Medicinal Plant Genomics website, formatted such that R can more easily read it in.

To run the script, set the directory to the working directory within R and simply run:

source(som.R)

This is the recommended way of running the script as it will prompt the user to input the number of clusters to select for further analysis.

The script requires the kohonen and fBasics packages. Specifically, it requires version 2.0.19 of the kohonen package, which can be installed as follows:

install.packages('devtools') # If devtools is not already installed
library(devtools)
install_version('kohonen', version='2.0.19')

It is reasonably trivial to update this script to use the newer versions of the kohonen package, but for the perposes of reproducability, the older version is used here.

References

Payne, R. M. E. et al. An NPF transporter exports a central monoterpene indole alkaloid intermediate from the vacuole. Nat. Plants 3, 16208 (2017).

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