Tasklist - Release 1.1.0

[AndiMunteanu]

This issue contains a list of tasks and fixes that need to be addressed until the next release.

Bug list / small improvements of the existing components

• fix the colour picking component for the case of more than 99 unique colours
• decide if we will stick with qualpalr for generating the palettes of colours, or switch to something such as randomcoloR, hues or colourlovers

Features

• add the option to select the continuous colour palettes in the shiny sandbox panel using paletteer
• add an option, near the Show config button, where the user could perform subsetting on the entire dataset based on metadata

Performance improvements

• ECS and ECC speedup
  • test if calculating the contingency matrix using dgTMatrix (with the two memberships being the i, j coords, and x a repeated 1) is faster
  • assess the impact of the calculation of minimum and maximum when calculating the contingency table
  • optimise the ECC based on the new contingency table function - generate the 1 vector only once, calculate the maximum and minimum only once
• improve the calculation of the rank matrix using sparse and dense matrix
• apply these improvements in a more generalisable way of applying the wilcoxon rank sum test

[Rohit-Satyam]

Am I allowed to add a few suggestions with respect to the documentation side of things?

1. Add citation file (reference.bib) so that the citations become clickable. Use

bibliography: references.bib
link-citations: yes

Some references are not clickable on the Index page. Also for installation, maybe you can mention something like install.packages(setdiff(cranpkgs, rownames(installed.packages())), dependencies = TRUE).
2. Append lines containing "Note:" with > sign to make them stand out.
3. Turn off warnings and excessive messages with arguments as given below:

knitr::opts_chunk$set(
  collapse = TRUE,cache = TRUE, warning = FALSE,message = FALSE,
  comment = "#>"
)

4. To help users distinguish arguments from functions, use () next to functions in the text. This also helps pkgdown link the function to the respective help page even when they come from different package.
5. In stability-pipeline-shiny.html use {-} after session.
6. This link doesn't work: https://mohorianulab.org/shiny/ClustAssess/clustassess_immune/