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# iSEEhex
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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.
