search

gamcil / clinker

Gene cluster comparison figure generator
MIT License
507 stars 66 forks source link

cluster similarity matrix #69

Open azazelsan opened 3 years ago

azazelsan commented 3 years ago

Hi Cameron, is there a way I can check the cluster similarity matrix raw data? Inkedfigure_LI

gamcil commented 3 years ago

Not currently, but a couple of people have asked for this so I'll try and add it to the next release.

azazelsan commented 3 years ago

Looking forward to it! A really great tool! Thanks!

gamcil commented 2 years ago

Hi @azazelsan, sorry it took so long but I've added the -mo, --matrix_out argument in clinker v0.0.22 to do this. For instance, using the clusters in the examples folder of the repository it generates a CSV file which looks like:

A. alliaceus CBS 536.65 A. burnettii MST-FP2249 A. mulundensis DSM 5745 A. versicolor CBS 583.65 P. vexata CBS 129021
A. alliaceus CBS 536.65 0.0 0.0 0.22350406073456497 0.3042042558254481 0.6034166451441612
A. burnettii MST-FP2249 0.0 0.0 0.23137351943160522 0.3408531051603084 0.6204295216720592
A. mulundensis DSM 5745 0.22350406073456497 0.23137351943160522 0.0 0.35355579358610445 0.6219765052472899
A. versicolor CBS 583.65 0.3042042558254481 0.3408531051603084 0.35355579358610445 0.0 0.6141102008013652
P. vexata CBS 129021 0.6034166451441612 0.6204295216720592 0.6219765052472899 0.6141102008013652 0.0