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AliTVTeam / AliTV

Visualize whole genome alignments as linear maps
https://alitvteam.github.io/AliTV/d3/AliTV.html
MIT License
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Cannot add phylogenetic tree #176

Closed swmuyu closed 2 years ago

swmuyu commented 2 years ago

Dear team aliTV, I run the code with the “chloroset” data and it generates json file successfully. But when I import the json file into the web page, the page is blank.

yml_and_json_file.zip

iimog commented 2 years ago

Hi swmuyu, I can reproduce the error. Unfortunately, I was not able to promptly find a solution. I'll have a closer look on Monday.

iimog commented 2 years ago

So I had a close look, and it seems like the names in the tree don't match the names you provide for the genomes. So in the addtree.yml You use names like Cistanche_phelypaea.fasta but in the tree file, the name seems to be only Cistanche_phelypaea. Note that you can define Cistanche_phelypaea as the name and Cistanche_phelypaea.fasta as the sequence_file like this:

genomes:
  - name: Cistanche_phelypaea
    sequence_files:
      - Cistanche_phelypaea.fasta
...

It is essential, however, that the genome names exactly match the names in the tree file. Another problem is, that you provide Nicotiana_tabacum as three different genomes (Nicotiana_tabacumA.fasta, Nicotiana_tabacumB.fasta, Nicotiana_tabacum.fasta) in this case all three genome variants would need to be included in the yml file.

swmuyu commented 2 years ago

So I had a close look, and it seems like the names in the tree don't match the names you provide for the genomes. So in the addtree.yml You use names like Cistanche_phelypaea.fasta but in the tree file, the name seems to be only Cistanche_phelypaea. Note that you can define Cistanche_phelypaea as the name and Cistanche_phelypaea.fasta as the sequence_file like this:

genomes:
  - name: Cistanche_phelypaea
    sequence_files:
      - Cistanche_phelypaea.fasta
...

It is essential, however, that the genome names exactly match the names in the tree file. Another problem is, that you provide Nicotiana_tabacum as three different genomes (Nicotiana_tabacumA.fasta, Nicotiana_tabacumB.fasta, Nicotiana_tabacum.fasta) in this case all three genome variants would need to be included in the yml file.

Thanks for your reply. I have successfully added the phylogenetic tree according to your instructions.

iimog commented 2 years ago

Awesome!