Samples not plotted

[bheimbu]

Dear @acvill,

really nice Shiny app you did but I've some problems to plot all my samples (see below). I'm really not sure what's the issue here? When I open the samples that not get plotted by bracken_plot in Pavian, I see that those samples actually have reads assigned, in some cases a lot. Find here
the output of combine_bracken_outputs.py and the kraken2 report files.

Cheers Bastian

[bheimbu]

Hi @acvill,

may the problem be that some samples do not have any reads assigned to the species level? However, this doesn't apply for every sample which aren't plotted above; some of which have more than 10 reads assigned to a certain species but still are not plotted.

Cheers Bastian

[acvill]

Hi Bastian,

Thanks for using bracken_plot. I took a look at your combined species-level bracken report, and it appears that some of your sample columns indeed sum to zero.

readr::read_tsv(file = "MIDORI2_GB261_0.2_S.txt", col_names = TRUE) |>
  tidyr::pivot_longer(cols = -c("name","taxonomy_id","taxonomy_lvl"), names_to = "sample") |> 
  dplyr::filter(!grepl("_num", sample)) |>
  dplyr::mutate(sample = gsub("_frac","",sample)) |>
  dplyr::group_by(sample) |>
  dplyr::summarize(sum = sum(value)) |>
  dplyr::filter(sum == 0) |>
  dplyr::pull(sample)

 [1] "WAL-F-1"  "WAL-F-3"  "WAL-F-4"  "WAL-F-5"  "WAL-L-1"  "WAL-L-2"  "WAL-L-5"  "WEI-AH-1" "WEI-AH-2" "WEI-AH-3" "WEI-AH-4" "WEI-AH-5"
[13] "WEI-F-1"  "WEI-F-2"  "WEI-F-3"  "WEI-F-4"  "WEI-F-5"  "WEI-L-1"  "WEI-L-2"  "WEI-L-3"  "WEI-L-5"  "ZIE-AH-2" "ZIE-AH-3" "ZIE-AH-5"
[25] "ZIE-F-1"  "ZIE-F-2"  "ZIE-F-3"  "ZIE-F-4"  "ZIE-F-5"  "ZIE-L-1"  "ZIE-L-2"  "ZIE-L-3"  "ZIE-L-4"  "ZIE-L-5"

Best,
Albert