---
layout: default
title: Cytoscape tutorials
nav_order: 3
has_children: true
version: latest
usemath: true
---
# `microbetag` on Cytoscape
microbetag web-app v1.0.1
MGG v1.0.0
```{note}
INPUT FILES AND PARAMETERS SETTING
Please, download the files required for the different cases and **set the parameters as shown in this tutorial**.
Parameters are essential especially for the online version of `microbetag` as they can lead either to non-optimal annotations or even failures of the software.
You may check the [FAQs](../faq.md) section for rules of thumb on how to set your parameters and you are always welcome to [join us on Matrix](https://matrix.to/#/#microbetagcommunity:matrix.org) and ask us directly.
```
We show how to install and use the microbetag Cytoscape app (called `MGG`) and use it with your data to get `microbetag`-annotated networks
using the `microbetagDB` and the online version of `microbetag`.
We also highlight the `MGG` features that allow you to go through the nodes and the edges annotations returned.
From the main menu box, you will have access to all features of the app.
As you see, the *Get Annotated Network* is currently not a clickable option.
That is because *microbetag* has no input yet.
You need first to feed the app with your abundance table and, if available, your co-occurrence network.
In both cases though, the **abundance table** will be **required**.
Please, make sure your taxonomy fits the criteria for `microbetag` to run.
You may find more on that issue on the [*Input files*](../input.md#input-files) section.
Then, as you will see in the following two cases, you will have to set the values to a set of parameters to describe your input data but also what annotation steps you would like `microbetag` to perform.
|Parameter | Variable | Description | Value |
|----------|---------------|-----------------------------------|-------|
|Choose input type |`input_category`| In case you already have a network, set it as `network` and load it; otherwise set it as `abundance_table`. In both cases you need to provide the abundance table though| [`abundance_table` \| `network`] |
|Choose taxonomy database| `taxonomy` | In case a user's taxonomy is to be used, denotes which taxonomy scheme to be used from microbetag | [`GTDB` \| `dada2` \| `qiime2`] |
|phenDB annotations | `phenDB` | return phenotypic traits based on phen models | bool |
|FAPROTAX annotations | `faprotax` | return annotations using the FAPROTAX database | bool |
|Pathway Complementarity | `pathway_complement`| return pathway complementarities between associated nodes | bool |
|Seed scores and complements| `seed_scores` | return complementarity and cooperation scores based on metabolic reconstructions seed sets | bool |
|Network clustering | `manta` | return clusters of nodes on the network using the manta package | bool |
|Consider children taxa | `get_children` | use genomes of children taxa of the taxa in the abundance table based on the NCBI Taxonomy scheme, relevant only if you use `Other` taxonomy | bool |
|heterogeneous | `heterogeneous` | (FlashWeave) enable heterogeneous mode for multi-habitat or -protocol data with at least thousands of samples (`FlashWeaveHE`) | bool |
|sensitive | `sensitive` | (FlashWeave) enable fine-grained associations (`FlashWeave-S`, `FlashWeaveHE-S`), sensitive=false results in the fast modes `FlashWeave-F` or `FlashWeaveHE-F` | bool |
The column `Variables` in the above table provides the variable names you need to use in case you are about to use `microbetag` from Python (see [tutorial](../advanced_use/python.md)).
The datasets to be used in all cases except of the [*Using a network*](./from_net.md) tutorial, are subsets of abundance tables with no special biological meaning.
However, in the *Using a network* case, we do use the network of [Hessler et *al.* (2023)](https://doi.org/10.1038/s41467-023-40360-4) who we would like to thank for sharing their data.
```{toctree}
:maxdepth: 2
:caption: Tutorials
abd_only
abd_and_metadata
from_net
load