microViz discussions

[david-barnett]

👋 Welcome to the microViz discussion forum:

You can use discussions to:

• Ask questions ❓
• Share ideas 💡
• Talk to other users 💬

If you would like to report a bug 🐞 consider raising an issue instead. Preferably with a reproducible example.

Feature requests can be made in discussions or issues.

Thank you! 🙂

[rrwagner1]

Hi. I am running a differential abundance model in microViz on some fungal data using a philoseq object. I am writing a csv from taxatree_stats_get and would like it to spit out actual otu numbers in addition to/instead of taxa names. How can I do this? Below is my code. Thanks.

bosfun_log2prop <- bosque_fun.phyloseq%>%
  tax_fix(unknowns = c("Glomerales")) %>% 
  # prepend the 1st letter of the rank to each tax_table entry, to ensure all are unique
  tax_prepend_ranks() %>% 
  tax_transform(
    trans = "compositional", rank = "Species",
    add = "halfmin" # adds half the minimum observed abundance to all values
  ) %>% #  
  # for various statistical, biological, and practical reasons, let's strictly filter taxa
  tax_filter(min_prevalence = 0.01, use_counts = TRUE) %>% 
  tax_transform(
    trans = "log2", # pseudocount added earlier allows us to use a log transform
    chain = TRUE # chain = TRUE allows the 2nd transformation
  )

bosfun_log2prop
rank_names(bosfun_log2prop)

bosfun_treeStats <- bosfun_log2prop %>% 
  # run all the statistical models
  taxatree_models(
    ranks = c("Phylum", "Class", "Order", "Family", "Genus", "Species"),
    variables = c("Site.type" ), type = lm # modelling function
  ) %>% 
  # extract stats from the models
  taxatree_models2stats(.keep_models = TRUE) %>%
  # adjust the p values for multiple testing, within each rank
  taxatree_stats_p_adjust(method = "BH", grouping = "rank")
bosfun_treeStats

taxatree_stats_get(bosfun_treeStats)

write_csv(taxatree_stats_get(bosfun_treeStats), "./data/processed/log2fold_fungal_out.csv")

[david-barnett]

Hi @rrwagner1

You could add OTU as a rank, e.g. see below a modified version of your code with 3 edited lines.

Hope this helps
David

bosfun_log2prop <- bosque_fun.phyloseq%>%
  tax_fix(unknowns = c("Glomerales")) %>% 
  # prepend the 1st letter of the rank to each tax_table entry, to ensure all are unique
  tax_prepend_ranks() %>% 
  tax_names2rank("OTU") %>%  # <- MODIFIED
  tax_transform(
    trans = "compositional", rank = "OTU",  # <- MODIFIED
    add = "halfmin" # adds half the minimum observed abundance to all values
  ) %>% #  
  # for various statistical, biological, and practical reasons, let's strictly filter taxa
  tax_filter(min_prevalence = 0.01, use_counts = TRUE) %>% 
  tax_transform(
    trans = "log2", # pseudocount added earlier allows us to use a log transform
    chain = TRUE # chain = TRUE allows the 2nd transformation
  )

bosfun_log2prop
rank_names(bosfun_log2prop)

bosfun_treeStats <- bosfun_log2prop %>% 
  # run all the statistical models
  taxatree_models(
    ranks = c("Phylum", "Class", "Order", "Family", "Genus", "Species", "OTU"),  # <- MODIFIED
    variables = c("Site.type" ), type = lm # modelling function
  ) %>% 
  # extract stats from the models
  taxatree_models2stats(.keep_models = TRUE) %>%
  # adjust the p values for multiple testing, within each rank
  taxatree_stats_p_adjust(method = "BH", grouping = "rank")
bosfun_treeStats

taxatree_stats_get(bosfun_treeStats)

write_csv(taxatree_stats_get(bosfun_treeStats), "./data/processed/log2fold_fungal_out.csv")

[rrwagner1]

Hi, David.

Thank you. That gets me closer. What I was hoping to get was another column from write_csv(taxatree_stats_get(bosfun_treeStats), "./data/processed/log2fold_fungal_out.csv") between term and taxon with the OTU# for that taxon. Is that possible?

Rich

[david-barnett]

Hi Rich,

I think either what you want is not possible, or I don't understand what you want

For example, where a taxon is classified at the Genus level, e.g. Bacteroides, there will be numerous OTU numbers that correspond to Bacteroides, not just one

does that help?

best
David