diff --git a/DESCRIPTION b/DESCRIPTION index d8bcd23..038dbfe 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: geposan Title: Gene Position Analysis -Version: 1.0.0 +Version: 1.1.0 Authors@R: person( "Elias", @@ -28,9 +28,7 @@ Imports: rlang, progress Suggests: - biomaRt, - httr, plotly, rlog, - stringr, + RMariaDB, usethis diff --git a/R/plots.R b/R/plots.R index 706a4ed..7971c10 100644 --- a/R/plots.R +++ b/R/plots.R @@ -718,8 +718,9 @@ plot_scores_by_position <- function(ranking, "Percentile: {round(percentile * 100, digits = 2)}%" ), marker = list( - color = base_color(), - size = 5 + size = 3, + color = "#919191", + opacity = 0.5 ), hoverinfo = "text" ) |> diff --git a/README.md b/README.md index 37fa0a1..b49574f 100644 --- a/README.md +++ b/README.md @@ -17,6 +17,17 @@ remotes::install_github("johrpan/geposan") See [this page](https://remotes.r-lib.org/reference/install_git.html) for more information on this command. +## Publication + +This method and its implementation have been peer-reviewed and published in +NAR Genomics and Bioinformatics. If you use the package in your research or +would like to refer to our methodology, please cite the following paper: + +Elias F Projahn, Georg Fuellen, Michael Walter, Steffen Möller, Proposing +candidate genes under telomeric control based on cross-species position data, +NAR Genomics and Bioinformatics, Volume 6, Issue 2, June 2024, lqae037, +https://doi.org/10.1093/nargab/lqae037 + ## Graphical interface Please also take a look at the interactive graphical web interface for geposan diff --git a/inst/CITATION b/inst/CITATION new file mode 100644 index 0000000..17d6334 --- /dev/null +++ b/inst/CITATION @@ -0,0 +1,11 @@ +bibentry( + bibtype = "Article", + title = "Proposing candidate genes under telomeric control based on cross-species position data", + author = "Elias F Projahn, Georg Fuellen, Michael Walter, Steffen Möller", + journal = "NAR Genomics and Bioinformatics", + year = 2024, + volume = 6, + number = 2, + pages = "lqae037", + doi = "10.1093/nargab/lqae037" +)