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Published 20 hours ago • verified publisher icon gamcil

cluster similarity matrix

Open azazelsan opened this issue 3 years ago • 3 comments

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

azazelsan avatar Jun 02 '21 21:06 azazelsan

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

gamcil avatar Jun 03 '21 07:06 gamcil

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

azazelsan avatar Jun 03 '21 21:06 azazelsan

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

gamcil avatar Oct 19 '21 06:10 gamcil