for counting and plotting KO groups of multiple organisms
This selection of scripts is designed to make tables of KO counts from IMG style KO counts tables
usage:
- Make a tree using the genome_tree_database. Around 50 genomes is a good number to display on a single A4 page.
- Go to IMG, and download the KO counts for each of the genomes in your tree. Save each as an individual text file in a new directory for this project somewhere. At the moment, the script requires the names of the files to match the ACE internal genome name from the database (ie, A00000012, C00000001).
- Run count_KEGG_KO_new.pl on this folder
- Run subset_KO_table_by_all_lists_new.pl on the output of (3).
- Run cbind_for_R_from_tree.pl on your tree (make sure you outgroup your tree, and make sure its in a format you are happy with (ARB or figtree can help with this)). Must be in newick format.
- Open generic_R_heatmaps_for_KO_tables.R in R or RStudio (I love RStudio, and you will too). modify the places that need mofidying, and make your heatmaps.
- Profit (significant profits may be taxed in coffee or lollies should these scripts be useful)