Add table of just ASVs explicitly mentioned in manuscript

rthanis · Feb 28, 2020 · 949f28f · 949f28f
1 parent ee1c13b
commit 949f28f
Show file tree

Hide file tree

Showing 2 changed files with 25 additions and 2 deletions.
diff --git a/analysis/export-asv-information.Rmd b/analysis/export-asv-information.Rmd
@@ -30,8 +30,18 @@ figure3_asvs <- c("ASV4", "ASV10", "ASV20", "ASV37", "ASV62", "ASV82",
 tb0 <- tb %>%
   filter(
     genus == "Clostridioides" | 
-    ncbi_species == "[Clostridium] hiranonis" | 
-    feature_id %in% figure3_asvs
+      ncbi_species == "[Clostridium] hiranonis" | 
+      feature_id %in% figure3_asvs
   )
 write_csv(tb0, here("results", "select-asv-sequences-and-taxonomy.csv"))
 ```
+and a minimal table without the low-prevalence C. hiranonis sequences,
+```{r}
+tb1 <- tb0 %>%
+  filter(
+    ncbi_species != "[Clostridium] hiranonis" |
+      is.na(ncbi_species) |
+      feature_id %in% c("ASV4", "ASV62")
+  )
+write_csv(tb1, here("results", "manuscript-asv-sequences-and-taxonomy.csv"))
+```
diff --git a/results/manuscript-asv-sequences-and-taxonomy.csv b/results/manuscript-asv-sequences-and-taxonomy.csv
@@ -0,0 +1,13 @@
+feature_id,sequence,kingdom,phylum,class,order,family,genus,species,ncbi_species
+ASV4,TACGTAGGGGGCTAGCGTTATCCGGATTTACTGGGCGTAAAGGGTGCGTAGGCGGTCTTTCAAGTCAGGAGTTAAAGGCTACGGCTCAACCGTAGTAAGCTCCTGATACTGTCTGACTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTAGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCACGAAAGCGTGGGGAGCAAACAGG,Bacteria,Firmicutes,Clostridia,Clostridiales,Peptostreptococcaceae,Peptoclostridium,NA,[Clostridium] hiranonis
+ASV10,TACGTAGGCGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGAGCGCAGGCGGGAAACTAAGCGGATCTTAAAAGTGCGGGGCTCAACCCCGTGATGGGGTCCGAACTGGTTTTCTTGAGTGCAGGAGAGGAAAGCGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCTAGGGTAGCGAACGGG,Bacteria,Firmicutes,Negativicutes,Selenomonadales,Veillonellaceae,Megamonas,funiformis,NA
+ASV20,TACGTAGGTGGCGAGCGTTATCCGGAATGATTGGGCGTAAAGGGTGCGTAGGTGGCAGATCAAGTCTGGAGTAAAAGGTATGGGCTCAACCCGTACTTGCTCTGGAAACTGATCAGCTAGAGAACAGAAGAGGACGGCGGAACTCCATGTGTAGCGGTAAAATGCGTAGATATATGGAAGAACACCGGTGGCGAAGGCGGCCGTCTGGTCTGGATTCTGACACTGAAGCACGAAAGCGTGGGGAGCAAATAGG,Bacteria,Firmicutes,Erysipelotrichia,Erysipelotrichales,Erysipelotrichaceae,Holdemanella,NA,NA
+ASV37,TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGAGGGAGCAGGCGGCAGCAAGGGTCTGTGGTGAAAGCCTGAAGCTTAACTTCAGTAAGCCATAGAAACCAGGCAGCTAGAGTGCAGGAGAGGATCGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCAGTGGCGAAGGCGACGATCTGGCCTGCAACTGACGCTCAGTCCCGAAAGCGTGGGGAGCAAATAGG,Bacteria,Firmicutes,Erysipelotrichia,Erysipelotrichales,Erysipelotrichaceae,Erysipelatoclostridium,ramosum,NA
+ASV62,TACGTAGGGGGCTAGCGTTATCCGGATTTACTGGGCGTAAAGGGTGCGTAGGCGGTCTTTCAAGTCAGGAGTTAAAGGCTACGGCTCAACCGTAGTAAGCTCCTGATACTGTCTGACTTGAGTGCAGGAGAGGAAAGTGGAATTCCCAGTGTAGCGGTGAAATGCGTAGATATTGGGAGGAACACCAGTAGCGAAGGCGGCTTTCTGGACTGTAACTGACGCTGAGGCACGAAAGCGTGGGGAGCAAACAGG,Bacteria,Firmicutes,Clostridia,Clostridiales,Peptostreptococcaceae,Peptoclostridium,NA,[Clostridium] hiranonis
+ASV82,TACGTAGGGGGCTAGCGTTATCCGGATTTACTGGGCGTAAAGGGTGCGTAGGCGGTCTTTCAAGTCAGGAGTGAAAGGCTACGGCTCAACCGTAGTAAGCTCTTGAAACTGGGAGACTTGAGTGCAGGAGAGGAGAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTTGCGAAGGCGGCTCTCTGGACTGTAACTGACGCTGAGGCACGAAAGCGTGGGGAGCAAACAGG,Bacteria,Firmicutes,Clostridia,Clostridiales,Peptostreptococcaceae,Clostridioides,difficile,NA
+ASV112,TACGTAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTCTGTAAGACAGATGTGAAATCCCCGGGCTCAACCTGGGAATTGCATTTGTGACTGCAGGACTAGAGTTCATCAGAGGGGGGTGGAATTCCAAGTGTAGCAGTGAAATGCGTAGATATTTGGAAGAACACCAATGGCGAAGGCAGCCCCCTGGGATGCGACTGACGCTCATGCACGAAAGCGTGGGGAGCAAACAGG,Bacteria,Proteobacteria,Gammaproteobacteria,Betaproteobacteriales,Burkholderiaceae,Sutterella,massiliensis/stercoricanis/wadsworthensis,NA
+ASV233,TACGTAGGGGGCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGTGCGTAGGTGGCATGGTAAGTCAGAAGTGAAAGCCCGGGGCTTAACCCCGGGACTGCTTTTGAAACTGTCATGCTGGAGTGCAGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTCACTGACACTGATGCACGAAAGCGTGGGGAGCAAACAGG,Bacteria,Firmicutes,Clostridia,Clostridiales,Lachnospiraceae,Anaerostipes,caccae,NA
+ASV331,TACGTAGGTGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGTGTAGGCGGGATTGCAAGTCAGATGTGAAAACTGGGGGCTCAACCTCCAGCCTGCATTTGAAACTGTAGTTCTTGAGTGCTGGAGAGGCAATCGGAATTCCGTGTGTAGCGGTGAAATGCGTAGATATACGGAGGAACACCAGTGGCGAAGGCGGATTGCTGGACAGTAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGG,Bacteria,Firmicutes,Clostridia,Clostridiales,Ruminococcaceae,Flavonifractor,plautii,NA
+ASV843,TACGTAGGGGGCTAGCGTTATCCGGATTTACTGGGCGTAAAGGGTGCGTAGGCGGTCTTTCAAGTCAGGAGTGAAAGGCTACGGCTCAACCGTAGTAAGCTCTTGAAACTGTAAGACTTGAGTGCAGGAGAGGAGAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTTGCGAAGGCGGCTCTCTGGACTGTAACTGACGCTGAGGCACGAAAGCGTGGGGAGCAAACAGG,Bacteria,Firmicutes,Clostridia,Clostridiales,Peptostreptococcaceae,Clostridioides,NA,NA
+ASV1962,TACGTAGGGGGCTAGCGTTATCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGTCTTTCAAGTCAGGAGTGAAAGGCTACGGCTCAACCGTAGTAAGCTCTTGAAACTGGGAGACTTGAGTGCAGGAGAGGAGAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTTGCGAAGGCGGCTCTCTGGACTGTAACTGACGCTGAGGCACGAAAGCGTGGGGAGCAAACAGG,Bacteria,Firmicutes,Clostridia,Clostridiales,Peptostreptococcaceae,Clostridioides,difficile,NA
+ASV2073,TACGTAGGGGGCTAGCGTTATCCGGATTTACTGGGCGTAAAGGGTGCGTAGGCGGTCTTTCAAGTCAGGAGTGAAAGGCTACGGCTCAACCGTATTAAGCTCTTGAAACTGGGAGACTTGAGTGCAGGAGAGGAGAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTTGCGAAGGCGGCTCTCTGGACTGTAACTGACGCTGAGGCACGAAAGCGTGGGGAGCAAACAGG,Bacteria,Firmicutes,Clostridia,Clostridiales,Peptostreptococcaceae,Clostridioides,difficile,NA