fix invalid class "GGbio" object: invalid object for slot "ggplot"

.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()

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,

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())
 

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)),

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
 ```