GitHub - iSEE/iSEEhex: iSEE extension for summarising data points in hexagonal bins (original) (raw)

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 fromCRAN. Then install iSEEhex fromBioconductor using the following code:

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

BiocManager::install("iSEEhex")

And the development version fromGitHub 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 iSEEapp that compares the ReducedDimensionHexPlot panel – defined in this package – to the standard ReducedDimensionPlot defined in theiSEE 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 citeiSEEhex.

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 actionsthrough usethis,remotes, and_rcmdcheckcustomized to use Bioconductor’s docker containers andBiocCheck_.
• Code coverage assessment is possible thanks tocodecov 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.