cal_abund, trans_abund$new and plot_bar does shows all classification in legends

[ShailNair]

I imported tsv files as dataframe and created an R6 object. Everything goes smoothly till I calculate abundance and plot barplots. Here when I specify a taxrank the plot will show all classifications pretending to that taxrank. e.g.

using delete_full_prefix = TRUE/FALSE in plot_bar does not make any difference

[ChiLiubio]

Hi, I can not make sure where the issue come from. Could you please provide more information, such as the codes you used and your microtable object dataset?

[ShailNair]

hi, Here is the data file data.zip

[ChiLiubio]

Hi, It is the prefix issue in the taxonomic table. In your tax_table of 'ms2', the prefix is like "k_" and "g_". In the previous version, this case was not covered in the function tidy_taxonomy function. However, double underlines are necessary in the functions of trans_abund. Now two solutions:

1. The function tidy_taxonomy has been optimized. Try to reinstall the microeco package from github. Then run your codes from this line: taxa2 %<>% tidy_taxonomy
2. If you donnot want to reinstall the package, you can change your prefix in taxa2 or ms2$tax_table to the format with double underlines, such as changing "k_" to "k__".

[ShailNair]

Thanks. I re-installed the microeco package and now the taxa labels are good