Loom 1.0

[JobLeonard]

Transcription of my notes on what needs to be fixed before Loom 1.0 is ready for the public. Only includes things that I have not already addressed (already fixed: optimising the search of dataset list, pasting genes interface, sorting of attribute keys, a number of heatmap/scatterplot/sparkline bugs).

Client

• [x] General:

  • [x] split Loompy, loom cli and loom server/browser into separate packages.
  • [x] Add filtering component to all views that shows which values are filtered out for which attribute (currently only visible in the Legend when an attribute is selected for coloring)
  • [x] Scrollbar bugs in Safari

• Sparkline

  • zoom option for post-release

• [x] Scatterplot

  • [x] more logical view settings
  • [x] quick settings (tSNE, PCS, SFDP, Log) as descriptive links, not buttons
  • [x] attribute selection for x/y/colors
  • axes post-1.0 release (scatterplots are mainly used for tSNE plots anyway)
  • [x] labels
  • [x] heatmap scale

• [ ] Introduction page

  • [ ] tutorials to explain usage and power user features
  • [ ] quick links
  • [ ] illustrative animated gifs

After all of the above has been implemented:

• [ ] Verify the website works in every (modern) browser on major desktop platforms
  • [x] Chrome (Mac, Linux, Windows)
  • [x] Firefox (Mac, Linux, Windows)
  • [ ] Safari (Mac)
  • [ ] Edge (Windows

Optional:

• selection of values (instead of filtering them out). Requires thinking about how to do so intuitively
• bookmarks view (more elaborate version of "share link"
• [x] fix dataset list "empty element" bug when clicking the navbar multiple time (visual bug, does not break anything)
• [x] fix Navbar visual bugs
• Scatterplot: implement edges (requires deep level retooling of Canvas component, perhaps better to merge with jump to interactive sketches instead of static plots)

Server

• [x] Heatmap Sorting

[JobLeonard]

part of making the functionalities more discoverable: adding tooltips

http://accessibility.athena-ict.com/aria/examples/tooltip.shtml

https://react-bootstrap.github.io/components.html#tooltips

[JobLeonard]

Prioritised roadmap based on Tuesday meeting:

• [x] Small fixes to the client
  • [x] Bring back high DPI support (Retina screens, etc)
  • [x] thicker sparklines
  • [x] bigger maximum scatterplot sprites (up to 128x128 from current 32x32 maximum)
  • [x] Legend icon
  • [x] pagination of dataset list reworked dataset-list UI
• [x] More involved fixes/improvements to the client
  • [x] limit scatterplot to 4 plots + matching UI improvements
  • [x] Settings bug in sparklines (must be something in how flexbox interacts with nested scrolling)
  • [x] axis labels (see #102)
  • [x] show list of which values are filtered out
• [x] Server
  • [x] Figure out why cloud server requires expansion and does not use fallback code
• [ ] Other
  • [ ] Test if the client works on all supported browsers (after above fixes)
  • [ ] Update documentation (see #81)
  • [x] make sure no sensitive data is left in the github repositories!

The above is enough for public release, after which we can implement other features:

• [ ] Interaction support for sparklines and scatterplot - see #79
  • [ ] lasso select
  • [ ] edges (low priority, requires layered plotting)
• [ ] Gene Lists
  • [ ] loompy: add data to new datasets
  • [ ] server: backwards compatible extraction
  • [ ] expansion code for gene lists
  • [ ] client:
  • [ ] new view
    • [ ] description (include markdown support)
    • [ ] "open selection in sparklines" (does it make sense to support scatterplots if we maximise the number of plots to four?)
  • [ ] "open selection from gene list" in sparklines

Really low priority:

• [ ] tutorial + bookmark/share link interface
• [x] offline storage of visited datasets

[JobLeonard]

New priority list, as per lab meeting and meeting with Sten today:

• [ ] Make it easier to get started
  • [ ] Safari dataset-list bug (see #121)
  • [x] windows installation without compilation (see #139)
  • [ ] when creating a new loom-datasets folder, it should also create two demo projects:
  • [x] /test/test.loom
  • [x] /Linnarsson Lab/cortex.loom (requires #132 to be closed)
  • [x] expansion page (see #114)
  • [x] documentation: installation instructions (see #81)
  • [x] (high priority)
• [ ] authentication support for private loom servers (see #32)
• [ ] auto-update when cache is out of sync with loom file (see #77)
  • [x] server: keep track if expansion has happened AFTER loom file modification
  • [x] client: empty cache when server says loom file has been modified, warn about expansion
• [x] grouped sparkline bug (see #61, #122)

Other enhancements (lower priority):

• [ ] documentation: tutorials (see #107)
• [ ] export selected genes to CSV or JSON (see #138)
• [ ] "save as A4/US Letter-sized PNG"(see #57)
• [ ] on-scatterplot labels (see #102)
• [ ] support for multiple layers
• [x] improve memory footprint (see #97)