csdaw / candidaev Goto Github PK

Currently, directory contents are displayed as such in README.md:

    .
    ├── ...
    ├── /directory1
    │    ├── /directory2     # Short description of contents
    │    ├── README.Rmd      # R markdown file to produce README.md
    │    └── README.md       # Description of /directory1 directory
    └── ...

Potentially change this to a table with the directory/folder name (and link) on the left and
the short description on the right.

For example:

I've added extra README.md (and corresponding README.Rmd) files to each directory in this repo to provide a detailed description of the contents of said directory and to explain how the contents can be used/viewed/downloaded.

It is important that these are added to .Rbuildignore so that (except the root README.md) they are not included when the package is built.

The plot_heatmap2 function which is modified from the plot_heatmap function from the DEP package works but is quite slow.

Perhaps removing some of the unnecessary (for this project) internal functions will speed it up.

Additionally, in future I need to update some of the old error messages.

The applications of plot_volcano2 are restricted due to overly specific assertions and because it requires a specific input format.

Need to rewrite to allow specification of columns with desired p-values and logFCs and labels for plotting.

The multiple na_filter functions in util.R are the same thing but with different operators e.g. &, <=, >=, etc.

They should be combined into a single function (should be relatively simple).

Root README.md will probably get longer in future.

Add a TOC to the top for easy navigation.