The iSEEu
package contains material and code that extends the iSEE
package (https://github.com/iSEE/iSEE).
We welcome contributions from the community, see below for more instructions. For example, during the Developer Day at the European Bioconductor 2019 conference (#EuroBioc2019
, at the UCLouvain, in Brussels, Belgium), we proposed a hackathon-like session, and we focused on the design of “modes”, i.e. preconfigured sets of panels and linked content to be used as starting setup when launching iSEE
.
iSEEu
can be easily installed from Bioconductor using BiocManager::install()
:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("iSEEu")
Optionally, if you want to install the development version from GitHub, you can use:
BiocManager::install("iSEE/iSEEu", dependencies = TRUE)
# or alternatively...
remotes::install_github("iSEE/iSEEu", dependencies = TRUE)
Setting dependencies = TRUE
should ensure that all packages, including the ones in the Suggests:
field of the DESCRIPTION
, are installed - this can be essential if you want to reproduce the code in the vignette, for example.
iSEE
universe with iSEEu
iSEE
first - the development version is recommended.
BiocManager::install("iSEE", version = "devel")
# or
remotes::install_github("iSEE/iSEE")
iSEEu
repo (https://github.com/iSEE/iSEEu) and clone it locally.make the desired changes in the files - start from the R
folder, then document via roxygen2
- and push to your fork.
once your contribution (function, panel, mode) is done, consider adding some information in the package. Some examples might be a screenshot of the mode in action (to be placed in the folder inst/modes_img
), or a well-documented example use case (maybe an entry in the vignettes
folder). Also add yourself as a contributor (ctb
) to the DESCRIPTION file.
make a pull request to the original repo - the GitHub site offers a practical framework to do so, enabling comments, code reviews, and other goodies.
more on documenting and code guidelines:
testthat
frameworkiSEE
?
Many of the “global” variables that are used in several places in iSEE
are defined in the constants.R script in iSEE
. We suggest to use these constants rather than hardcoding (e.g.) column names in the panel specification data frames, to protect against potential future changes of the precise column names. To access a constant, use iSEE:::.constantName
.
There are several modes already defined in the R/
directory.
Yes. Mainly guided by common sense of “never changing a working system”, please stick to the conventions we have been adopting for developing the existing codebase. A few simple style options:
git diff
operations easier to check.In addition to the eight standard panel types, custom panels are easily accommodated within iSEE
applications. For a guide, see the corresponding vignette. For examples, see this repo.
iSEE
for exploring other datasets/data types?
Yes, you can have a look at the examples in https://github.com/iSEE/iSEE_instances, where we tried to put together fully worked vignettes to re-analyze publicly available datasets, e.g. also trying to replicate some key visualizations of the original publications.
Please note that the iSEEu project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.