Enhancements

[PhilPalmer]

Enhancements

• 1) Input
  • File upload
    • Allow upload of pre-generated full dataframe
    • Allow re-upload of CSV files (implemented in 1f17a81 as part of Add example data #21)
    • Extract date + time & use that to determine plate numbers
    • Support other file formats eg messaging or renaming of input columns
  • Dilutions
    • Prevent dilutions table from overwriting plate data dilutions because horizontal dilutions will be required for ELLA
    • George: app crash when pasting too many dilutions App crashes if user pastes too many rows into dilutions table #28
  • Plate data
    • Make switching plates more intuitive
      • Change mouse numbers to start from mouse 6 on plate 2
      • Prevent plates overwiting one another when switching plates
    • Make all plates the same button
    • Add toggle to go betweeen RLU → types (would be implemented as part of Allow all features to be set using the plate data table #26)
    • Prevent the plate data from switching back to types when the dilutions are updated
    • Automatically increment all following plates if a user updates the mouse number in a previous plate
    • Conditional formatting (see here)
  • Other features
    • Sort feature levels such as subject
    • Change feature names (Update features names #24 )
      • Change name from primary -> virus
    • Section not clear to new users and so needs improvement!
      • Make app more robust if user hasn't entered all data eg title and report still work
      • Provide more guidance/feedback on which features need to be entered
      • Set default dropdown for incoluate to subject
    • Remove button
    • Make Submit button more visible and provide feedback once clicked
  • Performance
    • Reduce the number of uncessary calls resulting from reactivity
    • Improve the efficiency of the code which updates the types/subjects etc.
      • Replace nested for loops with vectors
      • Only update when changes occur
  • Add tooltips for help + improve messaging
  • Add example data (Add example data #21)
• 2) QC
  • Display no. of cells + no. of wells in av. luminescence values table
  • Plate heatmaps
    • Change row names to letters + add a key (for types)
    • Improve error handling eg when other features not set
  • Ask Joanne, Kelly & George re normalisation using cell + virus wells (plate vs global)
  • Update heatmaps automatically rather than on-click on new tab
  • Keep colour scheme consistent between plots
  • Stop errors showing underneath the types boxplot (Error message appears on QC Types Boxplot tab #27)
• 3) Results
  • Make plots interactive using plotly
  • Add plotly library declaration to raw R code
  • Create a separate plot for each primary!
  • Have option to change axis eg from -10 -> 110
  • Syntax hightling for raw R code
  • Support multiple primaries/viruses
  • Change Estimate -> IC50 Dilution in IC50 boxplot
  • Use multiple lines on the x-axis to show that it's a log scale
  • Show a loading spinner while the plots are loading
  • Have templates available for reports eg for Cambridge University / DIOSVax (knitr)
  • Have the option to update the colours used in the plot eg make PBS black
• Other
  • Refactoring (see here)
    • Use Shiny modules for each section of the app
    • Add a function and tests to ensure that the column types are correct
    • Create R package
    • Add tests (CI/CD)
    • Have auto-formatter like prettier
    • Reduce code duplication for plots in the app + code to display + in the Rmd
    • Add default_dilutions as parameter - if NULL then load data(defualt_dilutions)
    • On the show code tab do library(autoplate) and then use autoplate functions to generate the plot(s)
    • Improve the experience of using the library within R
    • Use Shiny modules for each section of the app
    • Generate documentation on the homepage from the readme
    • Add automatic code styling on PR with styler
    • Use shiny:: for all shiny functions so that shiny doesn't need to be loaded when the package is loaded
  • Update the readme - generate UI from markdown content
  • Diff assay types eg ELLA or ELISA or HIA assays
    • NA assay
      • ELISA reader input -> CSV
      • horizontal dilutions
      • support different and/or user defined custom plate templates
      • multiple mice per column eg rows C & D = mouse 2
  • Other (larger) plates eg 384-well plates
  • Custom features
  • Deploy to custom URL?
  • Pay for Shiny premium to get more app hours
  • Add a Rmd documentation web page similar to wpm (see here)