Some levels are missing

[Abelcanc3rhack3r]

Hi,
I was running the command line ktTextImport for this test file:
no. phylum class order origin

1 Bacteroidetes Bacteroidia Bacteroidales chromosome
1 unknown unknown unknown chromosome
1 Bacteroidetes Bacteroidia Bacteroidales chromosome
1 unknown unknown unknown chromosome
1 unknown unknown unknown chromosome
1 unknown unknown unknown chromosome
1 Bacteroidetes Bacteroidia Bacteroidales chromosome
1 unknown unknown unknown chromosome
1 Bacteroidetes Bacteroidia Bacteroidales chromosome
1 Bacteroidetes unknown unknown unknown
1 Bacteroidetes unknown unknown chromosome
1 Bacteroidetes Bacteroidia Bacteroidales chromosome
1 Bacteroidetes unknown unknown unknown
1 Bacteroidetes unknown unknown plasmid
1 Bacteroidetes Bacteroidia Bacteroidales chromosome
1 Bacteroidetes Bacteroidia Bacteroidales chromosome
1 Bacteroidetes Bacteroidia Bacteroidales chromosome
1 unknown unknown unknown chromosome
1 Bacteroidetes unknown unknown chromosome
1 Bacteroidetes Bacteroidia Bacteroidales chromosome
1 Bacteroidetes Flavobacteriia Flavobacteriales chromosome
1 Proteobacteria Gammaproteobacteria Enterobacterales plasmid

I got this krona plot

results4_krona_2.txt

There are a few problems with this plot:

1. The wedges for the Proteobacteria and unknown phylum are missing.
2. The classes bacteroidia and orders for the bacteroidetes are missing
3. The wedges for the unknown classes and orders are missing in the unknown phylum.

Can you guys help me diagnose this problem?

Thanks

[nvpatin]

I am having a similar problem with ktimporttext. The text file looks as follows:

fraction superkingdom phylum class order family genus species
0.006989827418079846 Eukaryota Viridiplantae:Chlorophyta Prasinophyceae Mamiellales Mamiellaceae Ostreococcus Ostreococcus lucimarinus
0.00264960273269132 d__Bacteria p__Proteobacteria c__Alphaproteobacteria o__Rhodobacterales f__Rhodobacteraceae g__LGRT01 s__LGRT01 sp001642945
0.002089908775655044 d__Archaea p__Thermoplasmatota c__Poseidoniia o__Poseidoniales f__Poseidoniaceae g__MGIIa-L1 s__MGIIa-L1 sp000246735
0.0019214235844647422 d__Bacteria p__Proteobacteria c__Gammaproteobacteria o__Pseudomonadales f__Halieaceae g__Luminiphilus s__Luminiphilus sp000169115

And the output html file has all the hits to domain Archaea (which all belong to one order, Poseidoniales) showing up at the domain level with Bacteria and Eukaryota:

This is the first time I've encountered this problem and have used ktimporttext many times on similar taxonomy files!

[thepatientwait]

Hello,

It's probably too late to help you both but I'm commenting so others don't have to spend as much time as I just did on this issue.

There's a check box on the left hand side of the html page named collapse.
This is ticked by default and will collapse all higher order levels if they only have one child taxon.
Just untick this box to see the missing levels.

Related issue: #182

These issues can probably me marked as resolved.