Siamcat2 interpretation plot (EBI-Metagenomics#20)

SHillman836 · Dec 8, 2022 · 74e2e1b · 74e2e1b
1 parent ba2dba2
commit 74e2e1b
Show file tree

Hide file tree

Showing 3 changed files with 95 additions and 59 deletions.
diff --git a/dependencies/mgnify-cache.tgz b/dependencies/mgnify-cache.tgz
diff --git a/dependencies/populate-mgnifyr-cache.R b/dependencies/populate-mgnifyr-cache.R
@@ -3,7 +3,10 @@ library(MGnifyR)
 
 mg <- mgnify_client(usecache = T, cache_dir = '/home/jovyan/.mgnify_cache')
 
-# For the "Comparative Metagenomics 1" notebook
+# For the "Comparative Metagenomics" notebook
 tara_all = mgnify_analyses_from_studies(mg, 'MGYS00002008')
 metadata = mgnify_get_analyses_metadata(mg, tara_all)
 
+# To generate phyloseq object
+clean_acc=c('MGYA00590456','MGYA00590543','MGYA00593110','MGYA00590477','MGYA00593125','MGYA00590448','MGYA00590508','MGYA00589025','MGYA00593139','MGYA00593220','MGYA00590525','MGYA00590534','MGYA00593112','MGYA00590498','MGYA00590535','MGYA00593223','MGYA00590480','MGYA00590496','MGYA00590523','MGYA00590444','MGYA00590517','MGYA00590575','MGYA00589039','MGYA00590574','MGYA00590474','MGYA00590554','MGYA00590469','MGYA00590471','MGYA00590522','MGYA00593141','MGYA00589049','MGYA00593123','MGYA00590564','MGYA00589024','MGYA00590572','MGYA00590545','MGYA00590518','MGYA00593126','MGYA00590526','MGYA00590500','MGYA00590570','MGYA00590520','MGYA00590443','MGYA00589013','MGYA00590449','MGYA00589021','MGYA00593130','MGYA00589047','MGYA00589042','MGYA00590577','MGYA00590470','MGYA00590473','MGYA00593216','MGYA00590562','MGYA00590464','MGYA00590484','MGYA00590462','MGYA00590565','MGYA00590439','MGYA00590472','MGYA00590566','MGYA00590552','MGYA00590485','MGYA00593133','MGYA00590544','MGYA00590455','MGYA00590437','MGYA00589044')
+ps = mgnify_get_analyses_phyloseq(mg, clean_acc)