wiscevan / automappa Goto Github PK

Some sort of indication of which contigs have marker genes on them **Maybe a different shaped point?

This would add a dash-mantine-component/transferlist component. This component could be used to allow the user fine-tuned control of which refinements to keep/delete for a given metagenome sample.

This would include the initial clustering results as well as the user refinements.

Feedback on whether this feature would be useful may necessary to follow-up with this implementation

To replace the default page tab icon, we simply need to add a favicon.ico file to /assets/favicon.ico.

Happy to receive any suggestions on what icon design we could use.

For starters, we could use an A? Maybe the same A that is in the Autometa logo animation?

There may be some helpful inspiration in KwanLab/Autometa#75

@samche42 Ideas welcome....

• Move contigs from bins that were not selected into unclustered

dash bootstrap component: Toast is likely what we want here.

The current docker image in the develop branch is only not compatible with AMD processors. It will be nice in terms of useability to make it compatible with different processors. This can be done using:

docker buildx build --platform linux/amd64,linux/arm64 --push -t WiscEvan/automappa:develop .

Add "download plot" button to each figure that allows user to download figure (in svg format) for publication-quality images.

Kind of like bandage mixed with current plots

Use would be to determine HGT and resolve contigs with highly different coverage

Refreshing the Dash page puts you back at square one, and any and all refinements are lost.

Eventually this can be refactored so when the layout is changing the entire figure does not need to be reconstructed... to do this we can initialize scatterplot-2d figure with contig embeddings using traces of their marker counts depicted with discrete marker symbols. Then add traces to the initialized fig corresponding to the color-by-column...

• initialize scatterplot with embeddings go.Scattergl(x=x_1, y=x_2)
• Initialize layout with minima and maxima of x and y axes
  (Will possibly need a store here relating to minima and maxima for each column that may reside on the x or y axes)
• add contig-marker-symbols to initialized scatterplot
• add colors to traces based on color-by-column

An example is performed with changing hovermode in the plotly docs

If there's any way to split a cluster of selected bins at a certain coverage level. Like if I select a mix bag of contigs that clearly need to be separated by coverage (e.g. one is around 10x cov and the other is around 2x cov, I could pick 5x cov and any contigs above that would go to refinement 1 and any with coverage below 5 would go to refinement 2.

Perhaps a modal of two boxes. One a dropdown of the math operator (gt, lt, gte, lte, eq, ne) and the other of the column (coverage, GC%, coding density, num markers)

After contigs are hidden, both scatterplots update their layouts to correspond to the new set coordinates minima and maxima.

• refactor scatterplot-2d layout
• refactor scatterplot-3d layout

Problem

Contigs that have already been manually curated are not displayed in the refinement table if you navigate away from (and then back to) the MAG Refinements tab.

Solution

When returning to the MAG refinements tab, the refinements table should be displayed and populated with the latest MAG refinement data

Self-explanatory issue title

Add bioconda recipe for Automappa so installation can be performed in a one-liner

conda install -c bioconda automappa

I installed automappa and autometa. When I run test files y received this error

Traceback (most recent call last):
  File "/media/microviable/d/miniconda/Automappa/bin/automappa", line 7, in <module>
    from automappa.__main__ import main
  File "/media/microviable/d/miniconda/Automappa/lib/python3.9/site-packages/automappa/__main__.py", line 4, in <module>
    from automappa import index
  File "/media/microviable/d/miniconda/Automappa/lib/python3.9/site-packages/automappa/index.py", line 20, in <module>
    from automappa.apps import mag_refinement, mag_summary
  File "/media/microviable/d/miniconda/Automappa/lib/python3.9/site-packages/automappa/apps/mag_refinement.py", line 12, in <module>
    from dash_extensions import Download
ImportError: cannot import name 'Download' from 'dash_extensions' (/media/microviable/d/miniconda/Automappa/lib/python3.9/site-packages/dash_extensions/__init__.py)

When Automappa was first written hidden divs were the suggested method to share data. However, now dcc.Store as well as some advanced caching techniques using flask_caching are now available and should provide significant speed-up. This may be a bit of work to wrap our heads around, but better to put this out there now to eventually be tackled than not suggested at all. 🤷

Here is the relevant dash documentation - dash -> sharing data between callbacks

Change index.py input argument so it only requires either the autometa output directory or binning main table

Rename the tabs as they are mentioned in the paper

• Rename Binning Exploration to MAG Refinement
• Rename Binning Summary to MAG Summary

For example, when it asks for a binning file, would be useful to know what Autometa usually names this as. My Autometa run happened to fail so the file I needed wasn't there. If it said something like *.binning.tsv that would help a user find the correct file, since Autometa outputs a lot of different files.

• Implement ability to upload metagenome annotations (together and/or separately)
• Implement ability to upload annotations corresponding to searched marker set(s)
• Component to group/display upload components (e.g. buttons w/modal or card etc.)

In regards to the last point, we will need to determine what interface feels most natural to the end user. (:raised_hands: hurrah :raised_hands: for the guinea pigs :wave:)

• dcc.Upload(...) component
• dbc.Modal(...) component
• dbc.Card(...) component

.... We could also add these into the offcanvas

I.e. after you have decided on your bin and saved the selection, those contigs disappear and cannot be placed into a different bin (Save the user from themselves here).

This tab would have buttons to login and select current and previously opened metagenomes

e.g.

• login
• overview
• upload

Existing metagenome datasets would be displayed with their details in a Card with a 2d scatterplot as the thumbnail.

Other info in the card would be hash, filename, modified date, etc.

This has been started on the home-tab branch

I actually have a script ready to go if you guys want it :) This was automatically generated by the very original Autometa and was super useful - especially when I was way too junior (read useless) to create my own script to find these stats.

The accepted way of assessing genome quality is via a combination of CheckM and the MIMAG standards. It throws novice users for a complete loop when the completeness/purity metrics in Automappa aren't reflected in subsequent CheckM quality checks.