Dash Bio apps - initial impressions

First-level impressions clicking through Dash Bio gallery beta apps: https://dash-gallery.plotly.host/dash-bio

Header

Would be great to have a GitHub link in the upper-right of the header that links to the code for each app on GitHub.

Dash Circos

• A lot of stuff in this sidebar. Pretty overwhelming. Maybe try organizing into tabs within the sidebar? Eg perhaps could organize tabs as, Data | Layout | Events | Upload

• Add a dropdown of a few different datasets?

Dash Clustergram

• Heatmap is a bit small. Maybe put the right-hand column on the left side instead, and try to make the clustergram go full-bleed to the right edge of the screen? Usually sidebars like this are on the left hand side.
• Would be nice to have a dropdown with a few classic clustergram data sets. Look at what the R clustergram packages and shiny apps use (eg heatmaply). Eg the mtcars dataset is a “classic:”

https://cran.rstudio.com/web/packages/heatmaply/vignettes/heatmaply.html

Dash Ideogram

• Needs margin on the left-hand side. Bugs me that controls are touching window edge.
• Make an issue in the original ideogram JS repo with a link to this app, to share and get feedback. Maybe will motivate the PI to address some of the issues you’ve raised.

Manhattan Plot

• Hover mode should be closest by default
• The “Visualize genome wide association studies…” description should should have a top margin so it’s not touch the top header.

Sequence Viewer

• Not sure what “Entry to view” is
• Might want a dropdown with a few other sequences besides insulin
• Would be great to combine this with 3d molecule viewer if there’s a way that makes sense
• vertical space between labels
• Sequence doesn’t wrap

Dash needle plot

• Labels such as Stem thickness are too large in font-size IMO.
• I only see one sample dataset in the dropdown - need to add more. A bunch here: https://github.com/jackparmer/react-needle-plot/tree/master/src/data On one of the Dash Bio calls I thought you had also found others in a Nature paper.
• Should be a left-side margin so that controls and labels don’t touch the edge of the window

Volcano

• This app doesn’t do much. Should maybe reduce the opacity of the points above the threshold? To make it more interesting, could add 2 overlaid histograms to the app - one histogram is all of the data and the other histogram is the data above the threshold. When the threshold is zero, the histograms are the same.
• Get rid of “Lower effect size” and “Upper effect size” controls. They just reset the x-axis range which I don’t think is very interesting.
• Set default hover mode to closest

Remaining apps

• @nchtra @jackluo @wilzbach Need your demo apps up here once your components are finished and merged

[shammamah-zz]

@matthewchan15 @Bachibouzouk Fernando gave us some great feedback - make sure that the dcc.Upload components have some text on them that clarifies that you’ll be able to click on it to open the file browser as well.

[Bachibouzouk]

I still can’t get the dropdown to show the 4 dataset options

@jackparmer , it is fixed in #51 which is waiting for @shammamah review 😃. You can preview the new app with the heroku deploy : https://dash-bio-test-pr-51.herokuapp.com/dash-bio/needle-plot