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lenaarenot committed Oct 18, 2024
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17 changes: 12 additions & 5 deletions topics/microbiome/tutorials/visualisation-ampvis/tutorial.md
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Expand Up @@ -83,11 +83,18 @@ or even a timeseries plot. Most of these visualisation methods are described in
"Overview of posible visualisation methods (taken from: Introduction to ampvis2 by Kasper Skytte Andersen)")

Your data need to be in an acceptable format for the ampvis_load tool. The tool
requires an OTU table and accepts the following formats: _phyloseq_, _biom_,
_dada2_sequencetable_ or _tabular_. The OTU table is the only mandatory input for
ampvis_load, but you can also input _sample_metadata_ (in _tabular_ or _tsv_ formats),
_taxonomy_table_ (in _tabular_ format), _fasta_file_ (in _fasta_ format)
and _phylogenetic_tree_ (in _newick_ format), as well as various combinations thereof.
requires an OTU table and accepts the following formats:
- _phyloseq_
- _biom_
- _dada2_sequencetable_
- _tabular_

The OTU table is the only mandatory input for ampvis_load, but you can also input:
- _sample_metadata_ (in _tabular_ or _tsv_ formats)
- _taxonomy_table_ (in _tabular_ format)
- _fasta_file_ (in _fasta_ format)
- _phylogenetic_tree_ (in _newick_ format)
- as well as various combinations thereof.

> <comment-title></comment-title>
> - If you work without taxonomy table, ampvis wouldn't be able to visualise taxonomy hierarchy and other options might be missing
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