iSEEhex

The goal of iSEEhex is to provide panels summarising data points in hexagonal bins for iSEE.

Installation instructions

Get the latest stable R release from CRAN. Then install iSEEhex from Bioconductor using the following code:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("iSEEhex")

And the development version from GitHub with:

BiocManager::install("iSEE/iSEEhex")

Example

For demonstration, we prepare an example SingleCellExperiment object.

library(scRNAseq)

# Example data ----
sce <- ReprocessedAllenData(assays="tophat_counts")
class(sce)
#> [1] "SingleCellExperiment"
#> attr(,"package")
#> [1] "SingleCellExperiment"

library(scater)
sce <- logNormCounts(sce, exprs_values="tophat_counts")

sce <- runPCA(sce, ncomponents=4)
sce <- runTSNE(sce)
rowData(sce)$ave_count <- rowMeans(assay(sce, "tophat_counts"))
rowData(sce)$n_cells <- rowSums(assay(sce, "tophat_counts") > 0)
sce
#> class: SingleCellExperiment 
#> dim: 20816 379 
#> metadata(2): SuppInfo which_qc
#> assays(2): tophat_counts logcounts
#> rownames(20816): 0610007P14Rik 0610009B22Rik ... Zzef1 Zzz3
#> rowData names(2): ave_count n_cells
#> colnames(379): SRR2140028 SRR2140022 ... SRR2139341 SRR2139336
#> colData names(23): NREADS NALIGNED ... passes_qc_checks_s sizeFactor
#> reducedDimNames(2): PCA TSNE
#> mainExpName: endogenous
#> altExpNames(1): ERCC

Then, we create an iSEE app that compares the ReducedDimensionHexPlot panel – defined in this package – to the standard ReducedDimensionPlot defined in the iSEE package.

library(iSEEhex)
#> Loading required package: iSEE
initialPanels <- list(
    ReducedDimensionPlot(
        ColorBy = "Feature name", ColorByFeatureName = "Cux2", PanelWidth = 6L),
    ReducedDimensionHexPlot(
        ColorBy = "Feature name", ColorByFeatureName = "Cux2", PanelWidth = 6L,
        BinResolution = 30)
)
app <- iSEE(se = sce, initial = initialPanels)

Citation

Below is the citation output from using citation('iSEEhex') in R. Please run this yourself to check for any updates on how to cite iSEEhex.

print(citation('iSEEhex'), bibtex = TRUE)
#> 
#> Rue-Albrecht K, Soneson C, Marini F, Lun A (2022). _iSEEhex_. doi:
#> 10.18129/B9.bioc.iSEEhex (URL:
#> https://doi.org/10.18129/B9.bioc.iSEEhex),
#> https://github.com/kevinrue/MyBioconductorPackage/iSEEhex - R package
#> version 0.99.0, <URL: http://www.bioconductor.org/packages/iSEEhex>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {iSEEhex},
#>     author = {Kevin Rue-Albrecht and Charlotte Soneson and Federico Marini and Aaron Lun},
#>     year = {2022},
#>     url = {http://www.bioconductor.org/packages/iSEEhex},
#>     note = {https://github.com/kevinrue/MyBioconductorPackage/iSEEhex - R package version 0.99.0},
#>     doi = {10.18129/B9.bioc.iSEEhex},
#>   }
#> 
#> Rue-Albrecht K, Soneson C, Marini F, Lun A (2018). "iSEE: Interactive
#> SummarizedExperiment Explorer." _F1000Research_, *7*, 741. doi:
#> 10.12688/f1000research.14966.1 (URL:
#> https://doi.org/10.12688/f1000research.14966.1), <URL:
#> https://f1000research.com/articles/7-741>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Article{,
#>     title = {iSEE: Interactive SummarizedExperiment Explorer},
#>     author = {Kevin Rue-Albrecht and Charlotte Soneson and Federico Marini and Aaron Lun},
#>     publisher = {F1000 Research, Ltd.},
#>     journal = {F1000Research},
#>     year = {2018},
#>     month = {Jun},
#>     volume = {7},
#>     pages = {741},
#>     doi = {10.12688/f1000research.14966.1},
#>     url = {https://f1000research.com/articles/7-741},
#>   }

Please note that the iSEEhex 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.

Code of Conduct

Please note that the iSEEhex project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Development tools

• Continuous code testing is possible thanks to GitHub actions through usethis, remotes, and rcmdcheck customized to use Bioconductor’s docker containers and BiocCheck.
• Code coverage assessment is possible thanks to codecov and covr.
• The documentation website is automatically updated thanks to pkgdown.
• The code is styled automatically thanks to styler.
• The documentation is formatted thanks to devtools and roxygen2.

For more details, check the dev directory.

This package was developed using biocthis.

Code of Conduct

Please note that the iSEEhex project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.