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README.md
<!-- README.md is generated from README.Rmd. Please edit that file --> # iSEEhex <!-- badges: start --> [![GitHub issues](https://img.shields.io/github/issues/iSEE/iSEEhex)](https://github.com/iSEE/iSEEhex/issues) [![GitHub pulls](https://img.shields.io/github/issues-pr/iSEE/iSEEhex)](https://github.com/iSEE/iSEEhex/pulls) [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) [![R-CMD-check-bioc](https://github.com/iSEE/iSEEhex/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/iSEE/iSEEhex/actions) [![Codecov test coverage](https://codecov.io/gh/iSEE/iSEEhex/branch/main/graph/badge.svg)](https://app.codecov.io/gh/iSEE/iSEEhex?branch=main) <!-- badges: end --> The goal of `iSEEhex` is to provide panels summarising data points in hexagonal bins for *[iSEE](https://bioconductor.org/packages/3.15/iSEE)*. ## Installation instructions Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `iSEEhex` from [Bioconductor](http://bioconductor.org/) using the following code: ``` r if (!requireNamespace("BiocManager", quietly = TRUE)) { install.packages("BiocManager") } BiocManager::install("iSEEhex") ``` And the development version from [GitHub](https://github.com/iSEE/iSEEhex) with: ``` r BiocManager::install("iSEE/iSEEhex") ``` ## Example For demonstration, we prepare an example *[SingleCellExperiment](https://bioconductor.org/packages/3.15/SingleCellExperiment)* object. ``` r 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](https://bioconductor.org/packages/3.15/iSEE)* app that compares the `ReducedDimensionHexPlot` panel – defined in this package – to the standard `ReducedDimensionPlot` defined in the *[iSEE](https://bioconductor.org/packages/3.15/iSEE)* package. ``` r 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**. ``` r 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](http://bioconductor.org/about/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](https://www.tidyverse.org/blog/2020/04/usethis-1-6-0/) through *[usethis](https://CRAN.R-project.org/package=usethis)*, *[remotes](https://CRAN.R-project.org/package=remotes)*, and *[rcmdcheck](https://CRAN.R-project.org/package=rcmdcheck)* customized to use [Bioconductor’s docker containers](https://www.bioconductor.org/help/docker/) and *[BiocCheck](https://bioconductor.org/packages/3.15/BiocCheck)*. - Code coverage assessment is possible thanks to [codecov](https://codecov.io/gh) and *[covr](https://CRAN.R-project.org/package=covr)*. - The [documentation website](http://iSEE.github.io/iSEEhex) is automatically updated thanks to *[pkgdown](https://CRAN.R-project.org/package=pkgdown)*. - The code is styled automatically thanks to *[styler](https://CRAN.R-project.org/package=styler)*. - The documentation is formatted thanks to *[devtools](https://CRAN.R-project.org/package=devtools)* and *[roxygen2](https://CRAN.R-project.org/package=roxygen2)*. For more details, check the `dev` directory. This package was developed using *[biocthis](https://bioconductor.org/packages/3.15/biocthis)*. ## Code of Conduct Please note that the iSEEhex project is released with a [Contributor Code of Conduct](http://bioconductor.org/about/code-of-conduct/). By contributing to this project, you agree to abide by its terms.