From d9b9baff2830d518afa8eb0af159b19a14cd8111 Mon Sep 17 00:00:00 2001 From: lenaarenot Date: Fri, 18 Oct 2024 11:29:29 +0200 Subject: [PATCH] bullet points of formats --- .../tutorials/visualisation-ampvis/tutorial.md | 17 ++++++++++++----- 1 file changed, 12 insertions(+), 5 deletions(-) diff --git a/topics/microbiome/tutorials/visualisation-ampvis/tutorial.md b/topics/microbiome/tutorials/visualisation-ampvis/tutorial.md index 5e62a85d9a42c..593e0b7b63722 100644 --- a/topics/microbiome/tutorials/visualisation-ampvis/tutorial.md +++ b/topics/microbiome/tutorials/visualisation-ampvis/tutorial.md @@ -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. > > - If you work without taxonomy table, ampvis wouldn't be able to visualise taxonomy hierarchy and other options might be missing