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firs edits based on KF comments
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hariszaf committed Aug 27, 2024
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7 changes: 6 additions & 1 deletion docs/faq.md
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Expand Up @@ -163,7 +163,7 @@ First, you can try to build a database with the closest genomes you can find for
If you do so, then you could run `microbetag` locally using those genomes as they were your bins.

Second, you could build a local instance of `microbetagDB` locally.
This would require a storage of $$ ~700GB $$.
This would require a storage of ~700GB.
<!-- REMEMBER! Edit next phrase once coplete -->
We are now working on an efficient way to go for that.

Expand All @@ -182,4 +182,9 @@ This is because `modelseedpy` requires RAST annotated genomes and thus it needs
Unfortunately, we have observed that this is not always stable.


## Can't import files on my macOS

Make sure you are not using aliases pointing to the files you need to import.
Sometimes you may use aliases even without knowing,
for example when you drag and drop a file on Finder, you create a shortcut of the file there, but the file is actually located in its original location.
Make sure you use the right path and not the shortcut when you are about to import a file on MGG.
2 changes: 2 additions & 0 deletions docs/mgg_tutorials/abd_only.md
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Expand Up @@ -46,6 +46,8 @@ You can view the imported data by clicking on the *Check Data Files* feature, fo
![check_abund_option](../../assets/images/app/checkOptionAbundData.png)

Once clicking that, a table will pop up where you can go through the data you have imported as the abundance table.
Keep in mind that in case you have more than a few samples, or your abundaces have a long number of digirs, you will need to double-click to a column at a time to be able to see its values.


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16 changes: 13 additions & 3 deletions docs/mgg_tutorials/roaming.md
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Expand Up @@ -21,11 +21,22 @@ Color-coding of the nodes (taxa) denoted the taxonomic level that a certain sequ
- <p style="color : Red">red</p> node was mapped to higher taxonomic level and no annotations were returned


If you edit the style of your *microbetag-*annotated network, you can always bring back its original style through the MGG main menu.
If you edit the style of your *microbetag*-annotated network, you can always bring back its original style through the MGG main menu.

![style](../../assets/images/app/visualStyle.png)


Now, if already opened, you need to open the MGG results panel; just click
`Apps > MGG > Show Results panel > Show results panel`
(see also [Loading models](../tutorials/load.md#load-already-microbetag-annotated-networks) tutorial).

Once your *microbetag*-annotated model is imported and the MGG results panel opened, you can now browse the network along with its annotations using both Cytoscape core features and those of MGG.

Notice that the MGG results panel on its bottom has two options:
the **Nodes** and the **Edges** panels.
By default, the **Nodes** panel is selected.
Let's start with that then!

By clicking on the *Show Species* button, all nodes that were not mapped to a genome will be masked.

![show_species](../../assets/images/app/showSpecies.png)
Expand Down Expand Up @@ -59,8 +70,7 @@ Edges are either



One may select from the two top buttons on the `Edges` panel to show only edges with pathway complementarities or seed complementarities.

Now, you can click on the **Edges** button on the bottom of the MGG panel to *jump* to the Edges annotations.

By clinking on a potential metabolic interaction edge,
the donor and the beneficiary species, along with their corresponding sequence identifiers will be displayed
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30 changes: 30 additions & 0 deletions docs/mgg_tutorials/save_annotated_net.md
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---
title: Save annotated network
layout: default
parent: Cytoscape tutorials
nav_order: 5
description: "tutorial on how to save your current work"
---

It is rather common for Cytoscape users to save the whole session they are working with as a `.cys` file by simply clicking on `File > Save Session As...` and giving a name to their session.

{: .warning}
Due to a buG in the current MGG implementation, if you save your `microbetag`-annotated network as a session, then you most probably will not be able to parse the seed and pathway complementarities **once you re-open** the session.

We already work on fixing the bug so we support this really handy Cytoscape feature.

Until then, one can save a `microbetag`-annotated network as described here, in order to have all the MGG features once they re-open it:

- Click on `File > Export >Network to File..`
- From the list of File Formats, select the `CX JSON (*.cx)` one
- Give a name to your `microbetag`-annotated network and press `OK`.

**Remember** that in this way, you only save the specific network and not all the networks you may have opened in your session!

{: .note}
You can always save your session normally, export the `microbetag`-annotated network as described above and when you want to open your session as it used to be, then you first load the session and from there you import the `.cx` file you exported. This will be *equivalent* with saving the whole original session.

Now you can re-open the `microbetag`-annotated network as descrobed [here](../tutorials/load.md#load-already-microbetag-annotated-networks).



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