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Navigating through a sorted file will make things easier (especially when dealing with positionned blocks, with while loops etc)

I've had a few users working with Barley Panache now. A request I have is an ability to highlight selected genes of interest, perhaps a tick box to show only genes being sorted by PAV so that it becomes easier to use a panel of genes in a single view for publication figures. Also an export/reporting feature of the selected gene regions to show PAV of that region, and the genes present with their percentage PAV. These would improve the functionality of Panache a lot. Thanks.

It is just slightly off with the fake data, and completely hides lines with real data. There must be a conversion problem between domain and range of the linearScale used there.

As for now the core threshold slider is rendered with svg, using fixed size. A better, more responsive approach would be to customize a slider from bootstrap to fit our needs.

Some genes are detected as overlapping with others while being on different chromosomes...

Here is an exemple with banana data, on chromosome 8, annotation located near the end of the coordinate system.

For coherence it would be better for CoreThreshold to take an updateStore function as a props instead of having it directly within it

[ Formerly issue 2 on the GitLab project ]

When hovering track below the presence absence matrix a tooltip with both text and background appears. This background does not fit the actual size of the text that is displayed.

For now the text is preprocessed in a canvas, then the size of that text is used to determine the size of the background and there is no direct link with the size of the displayed svg text.

We could either try to fix this (maybe some CSS conflicts ?) or modify the tooltips to use html tooltips instead of svg ones.

Sometimes special block with StartPosition < StartDisplay and EndPosition > EndDisplay exist and will not be registered for visualization, while they definitely should be on display. Filtering method could be improved to take such cases into account.

The main display view has a width based on the width of the screen when the app loaded.
Enabling resizing when the size of the window changes would be a nice addition. Implies the responsive resizing of PavMatrixAndTracks, OverlayedCanvas, AnnotationTrack and HollowAreaTrack

The coordinates retrieved by selecting an area with the 'Local pattern' sorting option does not seem to be properly stored (eg. being set at 0, instead of the actual left coordinate).
This could also be linked to errors with the gene PAV status sorting option, which somehow does not work for panBlocks without any gene?! See #32 (comment)

We should be able to use mouse wheel to scroll down or up through the pav matrix instead of having to rely only on the slider on the right.

For better display, the annotation track could be turned into a beeswarm plot, x positions would always be faithful to the data, and y position would be modified according to the available space.

Here is a nice example of how it could look : https://observablehq.com/@d3/beeswarm

Whe can keep square marks instead of the circles from the example

Default texts are fine, but they should be replaced when a file is loaded

Hi there,

Panache looks great -- thanks for offering this to the community!

I tried to get the demo server to work with your example data provided on the Wiki. I saved the data in the example table on the Wiki into a TSV file and tried to upload it to the demo server. The genotype tracks change from the default to B and C (what happens to A?), so this bit seems to work, but it doesn't appear to be picking up the chromosome numbers and consequently the dropdown chromosome selector is not populated with any values to choose from.
I have attached the file I used so you can reproduce this.

Many thanks
Micha

panache_test.txt

In order to limit the amount of svg on screen, Panache.vue should filter out the annotations that cannot be seen, cf filters already applied on pav data.

Right now annotation marks on AnnotationTrack are placed like this (left of annot <-> middlePos) :

Annot :              |||
Gene :    |----------|----------|

It should like this instead (middle of annot <-> middlePos) :

Annot :             |||
Gene :    |----------|----------|

Zoom level is used to change the display size in pixel of nucleotides. With a size too small, too many visual elements would be generated, making the whole app slower.
As for now the zoom level is too much focused on big or small sizes, and not enough on intermediate size (which would allowed about 40 columns on screen at once). This zoom scale, with the intermediate pivot could be better handled and adapted to the dataset on display.

As the tick scale starts at the very beginning of the svg container, its first number ( 0 ) is cut in half. Margins should be applied to see it in its entirety (maybe in a similar fashion to that of AnnotationCard)

To help user install Panache with their own data, an automated companion script that would take their PAV and GFF files as input and runs the parsing/conversions on it would be most useful.

Hi

I am having problems getting Panache to run.

I installed Docker and Docker compose and then ran bash ./start.sh

I get the following error:

## Populating apt-get cache...

+ apt-get update
Hit:1 http://security.debian.org/debian-security bullseye-security InRelease
Hit:2 http://deb.debian.org/debian bullseye InRelease
Hit:3 http://deb.debian.org/debian bullseye-updates InRelease
Reading package lists...

## Installing packages required for setup: lsb-release gnupg...

+ apt-get install -y lsb-release gnupg > /dev/null 2>&1

## Confirming "bullseye" is supported...

+ curl -sLf -o /dev/null 'https://deb.nodesource.com/node_13.x/dists/bullseye/Release'

## Your distribution, identified as "bullseye", is not currently supported, please contact NodeSource at https://github.com/nodesource/distributions/issues if you think this is incorrect or would like your distribution to be considered for support

ERROR: Service 'web' failed to build: The command '/bin/sh -c curl -sL https://deb.nodesource.com/setup_13.x | sudo -E bash -' returned a non-zero code: 1

I then try the npm route:

ubuntu@genome-browser:~/panache$ npm run build

> [email protected] build /home/ubuntu/panache
> vue-cli-service build


⠼  Building for production...
  When setting `useBuiltIns: 'usage'`, polyfills are automatically imported when needed.
  Please remove the direct import of `core-js` or use `useBuiltIns: 'entry'` instead.
⠏  Building for production...

 WARNING  Compiled with 5 warnings                                                                                                                    2:39:55 AM

 warning  in ./src/components/PavFileParser.vue?vue&type=script&lang=js&

"export 'group' (imported as 'd3') was not found in 'd3'

 warning  in ./src/components/GffFileParser.vue?vue&type=script&lang=js&

"export 'group' (imported as 'd3') was not found in 'd3'

 warning  

asset size limit: The following asset(s) exceed the recommended size limit (244 KiB).
This can impact web performance.
Assets: 
  js/chunk-vendors.f1c4b467.js (1.02 MiB)
  mediumFakeDataWithAllBlocks.tsv (705 KiB)
  MusaceaePangenome.tsv (1.97 MiB)
  BrassicaNapusForPanache.tsv (10 MiB)
  MusaceaePangenome_geneAnnot.gff (52.8 MiB)

 warning  

entrypoint size limit: The following entrypoint(s) combined asset size exceeds the recommended limit (244 KiB). This can impact web performance.
Entrypoints:
  app (1.36 MiB)
      css/chunk-vendors.48cb2c87.css
      js/chunk-vendors.f1c4b467.js
      css/app.a78752da.css
      js/app.0946853a.js


 warning  

webpack performance recommendations: 
You can limit the size of your bundles by using import() or require.ensure to lazy load some parts of your application.
For more info visit https://webpack.js.org/guides/code-splitting/

  File                                   Size              Gzipped

  dist/js/chunk-vendors.f1c4b467.js      1043.64 KiB       282.00 KiB
  dist/js/app.0946853a.js                130.14 KiB        34.67 KiB
  dist/css/chunk-vendors.48cb2c87.css    209.30 KiB        31.04 KiB
  dist/css/app.a78752da.css              9.04 KiB          2.44 KiB

  Images and other types of assets omitted.

 DONE  Build complete. The dist directory is ready to be deployed.
 INFO  Check out deployment instructions at https://cli.vuejs.org/guide/deployment.html

Are any of these warning messages of importance? It appears to be built using the npm method, but how do I deploy once the files are built in the dist directory?

In regards to the Docker method complaining about "bullseye" is that in regard to my Ubuntu version not being supported? I currently run Ubuntu 20.04.1 LTS.

The option panel (component LocalFilter) on the left of the screen should have the same length no matter how small or big the screen window is.

My pseudo rainbow color scale is nice and all, but does not follow vis science principles. I should either create a correct one or use a preexisting one that feets my needs.

Pav matrix is still quite small for now in order to work on it's sliders's behavior. It should return to reasonable size for production purposes.

Beige background of the AnnotationCard does not seem to fill in the entire grid element (there is a gap on the right) when used within Panache. In consequence its repositionning when displayed on the rightmost part of screen is also a bit off.

Hi

I have a GFA file and would like to convert to a compatible format for Panache to read in. I'm looking at using BioGraph.jl, however it isn't very clear in the documentation what exactly I need to do to get the correct format for Panache to use.

I've looked at the test_longest_path.jl in the test folder of BioGraph, but I'm not sure what the format output is supposed to be or if longest path is the correct approach to take. My GFA files are derived from PGGB. I want to use one of the references in the graph to refer to and include the GFF file from that single reference as well, including using that reference for the genomic coordinates. The way the PGGB graph was produced, no single genome was used as a reference as it was an all-to-all mapping. Thanks.

Annotation mark would be more eye pleasing with some colors. Related to the blocks below them ?
Plus the one annotation mark that displays an Annotation Card should be highlighted.

Hi,
I'd like to run Panache on my own laptop as well as a debian VM on a cloud. But when running the docker-compose up, I get the following error message :

Starting panache ... done
Attaching to panache
panache | Starting nginx: nginx.
panache | npm WARN read-shrinkwrap This version of npm is compatible with lockfileVersion@1, but package-lock.json was generated for lockfileVersion@2. I'll try to do my best with it!
panache | npm WARN deprecated [email protected]: The v1 package contains DANGEROUS / INSECURE binaries. Upgrade to safe fsevents v2
panache | npm ERR! code EBADPLATFORM
panache | npm ERR! notsup Unsupported platform for [email protected]: wanted {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"})
panache | npm ERR! notsup Valid OS:    darwin
panache | npm ERR! notsup Valid Arch:  any
panache | npm ERR! notsup Actual OS:   linux
panache | npm ERR! notsup Actual Arch: x64
panache | 
panache | npm ERR! A complete log of this run can be found in:
panache | npm ERR!     /root/.npm/_logs/2023-10-11T13_34_00_893Z-debug.log
panache exited with code 1

Looks like there is a problem with fsevents.

would you please help?
Best!