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

• General:

  • split Loompy, loom cli and loom server/browser into separate packages.
  • 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)
  • Scrollbar bugs in Safari

• Sparkline

  • zoom option for post-release

• Scatterplot

  • more logical view settings
    • quick settings (tSNE, PCS, SFDP, Log) as descriptive links, not buttons
    • attribute selection for x/y/colors
  • axes post-1.0 release (scatterplots are mainly used for tSNE plots anyway)
  • labels
  • 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
  • Chrome (Mac, Linux, Windows)
  • 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"
• fix dataset list "empty element" bug when clicking the navbar multiple time (visual bug, does not break anything)
• 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

• 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:

• Small fixes to the client
  • Bring back high DPI support (Retina screens, etc)
    • thicker sparklines
    • bigger maximum scatterplot sprites (up to 128x128 from current 32x32 maximum)
  • Legend icon
  • pagination of dataset list reworked dataset-list UI
• More involved fixes/improvements to the client
  • limit scatterplot to 4 plots + matching UI improvements
  • Settings bug in sparklines (must be something in how flexbox interacts with nested scrolling)
  • axis labels (see Axis and other scatterplot labels #102)
  • show list of which values are filtered out
• Server
  • 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 Update Documentation #81)
  • 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 Implementing a clean API for interactive plotters #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
• 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 Safari bug #121)
  • windows installation without compilation (see Getting loom to work from the Windows command line #139)
  • when creating a new loom-datasets folder, it should also create two demo projects:
    • /test/test.loom
    • /Linnarsson Lab/cortex.loom (requires Generate new cortex.loom with correct row order #132 to be closed)
  • expansion page (see Web-interface for expanding loom files #114)
  • documentation: installation instructions (see Update Documentation #81)
    • (high priority)
• authentication support for private loom servers (see Authentication #32)
• auto-update when cache is out of sync with loom file (see Keep cache synced with files #77)
  • server: keep track if expansion has happened AFTER loom file modification
  • client: empty cache when server says loom file has been modified, warn about expansion
• grouped sparkline bug (see Sparkline enhancements #61, [sparkline] avoid awkward small, uneven grouping, and confusing column stretching #122)

Other enhancements (lower priority):

• documentation: tutorials (see Tutorial Page #107)
• export selected genes to CSV or JSON (see Export selected genes to CSV #138)
• "save as A4/US Letter-sized PNG"(see Add "render print version" #57)
• on-scatterplot labels (see Axis and other scatterplot labels #102)
• support for multiple layers
• improve memory footprint (see Out of Memory issues for large datasets + large gene selections #97)