The goal of iSEEtree is to provide panels related to TreeSummarizedExperiment objects which facilitate the interactive visualisation of microbiome data in iSEE.
The development version of iSEEtree can be installed from GitHub as follow:
remotes::install_github("microbiome/iSEEtree")
In the future, this package may be submitted to Bioconductor.
The basic functionality of iSEEtree can be explored as follows:
library(iSEEtree)
library(mia)
library(scater)
# Import TreeSE
data("Tengeler2020", package = "mia")
tse <- Tengeler2020
# Add relabundance assay
tse <- transformAssay(tse, method = "relabundance")
# Add reduced dimensions
tse <- runMDS(tse, assay.type = "relabundance")
# Launch iSEE
if (interactive()) {
iSEE(tse)
}
Please note that iSEEtree was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package. In particular, iSEEtree implements the miaViz package for microbiome data visualisation to create panels that are specific for TreeSummarizedExperiment objects. Not surprisingly, it also depends on the generic panels from iSEE.
- Continuous code testing is performed on GitHub actions and include R CMD check, BiocCheck and testthat.
- Code coverage assessment is possible thanks to codecov.
- The documentation website is automatically updated thanks to pkgdown.
- The documentation is formatted thanks to devtools and roxygen2.
- All the actions above are made reproducible by rworkflows
This package was developed using usethis.
Please note that the iSEEtree project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms. If you come across a bug or see potential for improvement, feel free to open an issue and we will plan the next move. is missing or could be improved. If you are interested in contributing, you can check our issues and try to find a solution. Either way, contributions are very much appreciated.