csdaw / candidaev Goto Github PK
View Code? Open in Web Editor NEWResearch compendium package for Dawson et al. (2020)
License: MIT License
Research compendium package for Dawson et al. (2020)
License: MIT License
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:
File/folder | Short description |
---|---|
/R | Short description goes here |
/data-raw | Another short description |
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.
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