diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index a1fef09..071de2f 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -27,11 +27,11 @@ jobs: R_KEEP_PKG_SOURCE: yes steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - - uses: r-lib/actions/setup-pandoc@v1 + - uses: r-lib/actions/setup-pandoc@v2 - - uses: r-lib/actions/setup-r@v1 + - uses: r-lib/actions/setup-r@v2 with: r-version: ${{ matrix.config.r }} http-user-agent: ${{ matrix.config.http-user-agent }} @@ -44,11 +44,11 @@ jobs: sudo apt-get install --yes libcurl4-openssl-dev Rscript -e "install.packages('curl', repos='https://cloud.r-project.org')" - - uses: r-lib/actions/setup-r-dependencies@v1 + - uses: r-lib/actions/setup-r-dependencies@v2 with: extra-packages: rcmdcheck - - uses: r-lib/actions/check-r-package@v1 + - uses: r-lib/actions/check-r-package@v2 - name: Show testthat output if: always() diff --git a/DESCRIPTION b/DESCRIPTION index 554b667..c441a2f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: scruff Title: Single Cell RNA-Seq UMI Filtering Facilitator (scruff) -Version: 1.21.1 +Version: 1.27.1 Date: 2024-03-27 Authors@R: c(person("Zhe", "Wang", email = "zhe@bu.edu", @@ -20,7 +20,7 @@ Depends: R (>= 4.0) License: MIT + file LICENSE Encoding: UTF-8 LazyData: TRUE -RoxygenNote: 7.3.1 +RoxygenNote: 7.3.3 VignetteBuilder: knitr Imports: data.table, GenomicAlignments, @@ -47,7 +47,8 @@ Imports: data.table, SingleCellExperiment, SummarizedExperiment, Rsubread, - parallelly + parallelly, + patchwork Suggests: BiocStyle, knitr, diff --git a/R/rview.R b/R/rview.R index 9f00079..b30aea0 100644 --- a/R/rview.R +++ b/R/rview.R @@ -33,8 +33,8 @@ rview <- function(bamGA, S4Vectors::mcols(readsGr)$umi <- data.table::last( data.table::tstrsplit(names(readsGr), ":")) - g <- ggplot2::ggplot(readsGr) + - ggbio::geom_arrow(ggplot2::aes(color = umi)) + + g <- ggplot2::ggplot() + + ggbio::geom_arrow(data = readsGr, ggplot2::aes(color = umi)) + .themePublication() + ggplot2::theme(axis.title.y = ggplot2::element_blank()) diff --git a/R/scruffFunctions.R b/R/scruffFunctions.R index d149d22..5f4f0aa 100644 --- a/R/scruffFunctions.R +++ b/R/scruffFunctions.R @@ -386,9 +386,11 @@ size = ggplot2::rel(1), hjust = 0.5), text = ggplot2::element_text(), - panel.background = ggplot2::element_rect(color = NA), - plot.background = ggplot2::element_rect(color = NA), - panel.border = ggplot2::element_rect(color = NA), + panel.background = ggplot2::element_rect(fill = NA, + color = NA), + plot.background = ggplot2::element_rect(fill = NA, + color = NA), + panel.border = ggplot2::element_blank(), axis.title = ggplot2::element_text( face = "bold", size = ggplot2::rel(1)), diff --git a/vignettes/scruff.Rmd b/vignettes/scruff.Rmd index b0254de..3d063bc 100644 --- a/vignettes/scruff.Rmd +++ b/vignettes/scruff.Rmd @@ -26,6 +26,7 @@ suppressPackageStartupMessages(library(BiocStyle)) # For generation of these files, please refer to the Stepwise Tutorial. library(scruff) +library(patchwork) # Get the paths to example FASTQ, FASTA, and GTF files. # Please note that because the following files are included in @@ -220,9 +221,16 @@ data(bamExample, package = "scruff") start <- 1094 end <- 2675 -g1 <- rview(bamExample, chr = "MT", start = start, end = end) -g2 <- gview(gtf, chr = "MT", start = start, end = end) -g <- ggbio::tracks(g1, g2, heights = c(4, 1), xlab = "chr MT") +g1 <- rview(bamExample, chr = "MT", start = start, end = end) + + ggplot2::scale_x_continuous(limits = c(start, end)) +g2 <- gview(gtf, chr = "MT", start = start, end = end) + + ggplot2::scale_x_continuous(limits = c(start, end)) +g <- (g1 + ggplot2::theme(axis.title.x = ggplot2::element_blank(), + axis.text.x = ggplot2::element_blank(), + plot.margin = ggplot2::margin(t = 0, b = 0))) / + (g2 + ggplot2::theme(plot.margin = ggplot2::margin(t = 0, b = 0))) / + patchwork::plot_layout(ncol = 1, + heights = c(4, 1)) g ```