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fbreitwieser / pavian

🌈 Interactive analysis of metagenomics data
https://doi.org/10.1093/bioinformatics/btz715
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Errors when comparing across samples #76

Open pieterjanvc opened 3 years ago

pieterjanvc commented 3 years ago

Hi,

When I combine MetaPhlan 3 reports with Kraken / Centrifuge ones, I get an error at the across samples plot under the sample tab when clicking a specific taxon

ERROR 1

Can't join on `x$taxID` x `y$taxID` because of incompatible types.
i `x$taxID` is of type <integer>>.
i `y$taxID` is of type <character>>.

This error does not happen when using only Kraken / Centrifuge OR Metphlan, so I suspect the Metaphlan columns are read as different classes.

I attached 3 files ASF365 (.kr .cf .mf) to reproduce this error

ERROR 2 Another error in the same panel happens when I combine results from kraken / centrifuge that were generated with de novo artificial genome generators CAMISIM and grinder (I'm working on a project creating a new type of artificial metagenome generator and am comparing results). I don't think this should matter, as kraken and centrifuge did not throw any errors (just some warnings assigning certain seq to root)

factor level [2] is duplicated

I attached 2 files ASF_camisim.kr and ASF_camisim.cf reproduce this error

Thanks again for all the work you put into this app! If my paper gets published, this will mean another citation for your app though :)

Thanks, PJ

debugFiles.zip

nikolasbasler commented 2 years ago

I also experience Error 2 when looking at kraken2 results and I hover over a taxon. R version 4.1.2 shiny version 1.7.1 pavian version 1.2.0

sanderdebacker commented 2 years ago

Encountered the same errors with: R version 4.1.1 shiny version 1.7.1 pavian v1.0 Any progress on these errors?

landowark commented 1 year ago

I am also having the same problems doing Kraken2 analysis with: R: v4.2.1 pavian: v1.2.0 shiny: v1.7.2

The console gives the following output:

Warning: Error in levels<-: factor level [2] is duplicated 173: factor 171: plot_it 170: renderPlot 168: func 128: drawPlot 114: 98: drawReactive 85: renderFunc 84: output$sample-plot1 3: runApp 2: print.shiny.appobj 1:

Rohit-Satyam commented 6 months ago

Me too @fbreitwieser

R: 4.2.3 pavian:1.2.1 shiny: 1.80

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