Parsing BIOM1 format exported from MEGAN

[Denis Kutnjak]

Hi,

I am trying to parse the BIOM format file (attached here), exported from MEGAN. The version of the BIOM should be 1.0. 

I tried parsing the file directly by using parse_qiime_biom, however this gives me an error: 

Error in data.frame(..., check.names = FALSE) : 

  arguments imply differing number of rows: 0, 494

Do you think there is something I can do to import such file using this parser or I need to reformat it to another format somehow?

Thank you for help in advance, best,

Denis

[Zachary Foster]

Hello Denis,

Thanks for the report! I fixed it so it works with that file. Reinstall and try again:

devtools::install_github("ropensci/taxa")
devtools::install_github("grunwaldlab/metacoder")

Hopefully I can make this parser work with all biome files as people report problems. I will probably rename it parse_biome if that happens.

That taxonomy is pretty large, so if you looking to graph it, I suggest trimming off any parts you are not interested in using the `filter_taxa` function or plotting subsets (also using `filter_taxa`). Adding the heat_tree options `layout = "da", initial_layout = "re"` might help too.

> parse_qiime_biom("~/Downloads/test32.biom") %>%
+     heat_tree(
+         node_label = taxon_names,
+         node_size = n_obs,
+         node_color = n_obs,
+         layout = "da", initial_layout = "re"
+     )

[Denis Kutnjak]

Dear Zachary,

thank you very much for this fix and for a great software altogether! I like it very much!

Denis

[Zachary Foster]

Thanks Denis! I am glad it worked

-Zach