Bugs in visualization scripts

[michaelgruenstaeudl]

• [x] Bug in JenkeEtAl2024Table1.R, JenkeEtAl2024Table3.R, JenkeEtAl2024Table4.R, and JenkeEtAl2024Figure_2.pdf Since the Assembly Method cannot be parsed from all genome records, this column is sometimes missing from the NC_000000_SRA_meta.csv file. This currently throws the following error, because line 36 in the script cannot be executed (subtable_assembly <- get_table_1_subtable(cov_data, "Assembly Method"))

Error in `rename()`:
! Can't rename columns that don't exist.
✖ Column `Assembly Method` doesn't exist.
Backtrace:
     ▆
  1. ├─global create_table_1(cov_data)
  2. │ └─global get_table_1_subtable(cov_data, "Assembly Method")
  3. │   └─... %>% mutate(cumulative_percentage = cumsum(percentage))
  4. ├─dplyr::mutate(., cumulative_percentage = cumsum(percentage))
  5. ├─dplyr::mutate(., percentage = (count/sum(count)) * 100)
  6. ├─dplyr::summarize(., count = n(), evenness = mean(E_score), std = sd(E_score))
  7. ├─dplyr::group_by(., State)
  8. ├─dplyr::select(., -count)
  9. ├─dplyr::mutate(., `:=`(State, ifelse(count < 5, "missing", State)))
 10. ├─dplyr::ungroup(.)
 11. ├─dplyr::mutate(., count = n())
 12. ├─dplyr::group_by(., State)
 13. ├─dplyr::rename(., State = !!ensym(grouping))
 14. ├─dplyr:::rename.data.frame(., State = !!ensym(grouping))
 15. │ └─tidyselect::eval_rename(expr(c(...)), .data)
 16. │   └─tidyselect:::rename_impl(...)
 17. │     └─tidyselect:::eval_select_impl(...)
 18. │       ├─tidyselect:::with_subscript_errors(...)
 19. │       │ └─base::withCallingHandlers(...)
 20. │       └─tidyselect:::vars_select_eval(...)
 21. │         └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
 22. │           └─tidyselect:::eval_c(expr, data_mask, context_mask)
 23. │             └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
 24. │               └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
 25. │                 └─tidyselect:::as_indices_sel_impl(...)
 26. │                   └─tidyselect:::as_indices_impl(...)
 27. │                     └─tidyselect:::chr_as_locations(x, vars, call = call, arg = arg)
 28. │                       └─vctrs::vec_as_location(...)