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| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| Parent folder | |||
| scripts | 2018-07-19 | ||
| output | 2018-07-19 | ||
| inputs | 2018-07-16 | ||
| README.txt | 2018-07-19 | 1.1 kB | |
| Totals: 4 Items | 1.1 kB | 0 | |
In this folder, we provide our source codes used to produce counting matrices of taxons and functions to be clustered along with additional data, listed below. Folder inputs: contains one file that is used as input for Kaiju (kaiju_input.tar.gz) and two other files that were generated by Kaiju and Interpro tools and were used to generate counting matrices by the corresponding scripts. Folder output: contains the expected counting matrices output for the scripts (taxa.csv: all taxa found; taxa_30.csv: only top 30 taxa per sample; functions.csv: all proteins found) Folder scripts: contains five R scripts, described below: - taxonomic_analysis.R: produces the taxonomic matrix - taxonomic_cluster_plot.R: plots samples clustered by taxonomic composition - taxonomic_stacked_plot.R: plots taxonomic composition of each sample - functional_analysis.R: produces the functional matrix - functional_cluster_plot.R: plots samples clustered by functions See our wiki for more details about this project: https://sourceforge.net/projects/corumba/wiki