From 5fddd9d1aeeb79314024821844295435c0d0bd72 Mon Sep 17 00:00:00 2001 From: HDash <16350928+HDash@users.noreply.github.com> Date: Fri, 18 Oct 2024 13:13:18 +0100 Subject: [PATCH] Update viridis scale --- DESCRIPTION | 2 +- R/plot_chromHMM.R | 2 +- R/tidy_chromosomes.R | 2 +- README.md | 2 +- man/tidy_chromosomes.Rd | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 768d88a..1354de8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Type: Package Package: EpiCompare Title: Comparison, Benchmarking & QC of Epigenomic Datasets -Version: 1.9.6 +Version: 1.9.7 Authors@R: c( person(given = "Sera", family = "Choi", email = "serachoi1230@gmail.com", diff --git a/R/plot_chromHMM.R b/R/plot_chromHMM.R index dd7c4b0..7672d56 100644 --- a/R/plot_chromHMM.R +++ b/R/plot_chromHMM.R @@ -102,7 +102,7 @@ plot_chromHMM <- function(peaklist, fill = value)) + ggplot2::ylab("") + ggplot2::xlab("") + - ggplot2::scale_fill_viridis_b() + + ggplot2::scale_fill_viridis_c() + ggplot2::theme_minimal() + ggplot2::theme(axis.text = ggplot2::element_text(size = 11)) + ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 315, diff --git a/R/tidy_chromosomes.R b/R/tidy_chromosomes.R index 8c94547..1da0f17 100644 --- a/R/tidy_chromosomes.R +++ b/R/tidy_chromosomes.R @@ -35,7 +35,7 @@ #' @examples #' # make a GRanges #' chrom <- c("chr2", "chr3", "chrX", "chrY", "chrM", "junk") -#' gr <- GRanges(seqnames = chrom, +#' gr <- GenomicRanges::GRanges(seqnames = chrom, #' ranges = IRanges(start = 2*(1:6), end = 3*(1:6)), #' strand = "+", #' seqinfo = Seqinfo(chrom)) diff --git a/README.md b/README.md index 2a288be..17fbfc7 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ GPL-3](https://img.shields.io/badge/license-GPL--3-blue.svg)](https://cran.r-project.org/web/licenses/GPL-3) [![](https://img.shields.io/badge/doi-https://doi.org/10.1101/2022.07.22.501149-blue.svg)](https://doi.org/https://doi.org/10.1101/2022.07.22.501149)
-[![](https://img.shields.io/badge/devel%20version-1.9.6-black.svg)](https://github.com/neurogenomics/EpiCompare) +[![](https://img.shields.io/badge/devel%20version-1.9.7-black.svg)](https://github.com/neurogenomics/EpiCompare) [![](https://img.shields.io/github/languages/code-size/neurogenomics/EpiCompare.svg)](https://github.com/neurogenomics/EpiCompare) [![](https://img.shields.io/github/last-commit/neurogenomics/EpiCompare.svg)](https://github.com/neurogenomics/EpiCompare/commits/master)
[![R build diff --git a/man/tidy_chromosomes.Rd b/man/tidy_chromosomes.Rd index 0f48aaf..a4d0389 100644 --- a/man/tidy_chromosomes.Rd +++ b/man/tidy_chromosomes.Rd @@ -46,7 +46,7 @@ Standard chromosomes are defined using the \examples{ # make a GRanges chrom <- c("chr2", "chr3", "chrX", "chrY", "chrM", "junk") -gr <- GRanges(seqnames = chrom, +gr <- GenomicRanges::GRanges(seqnames = chrom, ranges = IRanges(start = 2*(1:6), end = 3*(1:6)), strand = "+", seqinfo = Seqinfo(chrom))