Update to Bioc 3.23/R 4.6, resolve R CMD check warnings, and fix BiocCheck errors

.github/workflows/check-bioc-devel.yml

@@ -265,7 +265,8 @@ jobs:
               dir('check', 'tar.gz$', full.names = TRUE),
               `quit-with-status` = TRUE,
               `no-check-R-ver` = TRUE,
-              `no-check-bioc-help` = TRUE
+              `no-check-bioc-help` = TRUE,
+              `no-check-version-num` = TRUE
           )
         shell: Rscript {0}
 

DESCRIPTION

@@ -2,17 +2,28 @@ Package: plotgardener
 Title: Coordinate-Based Genomic Visualization Package for R
 Version: 1.15.1
 Date: 2024-06-28
-Author: Nicole Kramer [aut, cre], Eric S. Davis [aut], Craig Wenger [aut],
-    Sarah Parker [ctb], JP Flores [ctb], Erika Deoudes [art], Michael Love [ctb],
-    Douglas H. Phanstiel [aut, cre, cph]
-Maintainer: Nicole Kramer <nekramer27@gmail.com>,
-            Douglas Phanstiel <douglas_phanstiel@med.unc.edu>
+Authors@R: c(
+    person("Nicole", "Kramer", email = "nekramer27@gmail.com",
+           role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0001-9617-9671")),
+    person("Eric S.", "Davis", email = "esdavis@live.unc.edu",
+           role = "aut",
+           comment = c(ORCID = "0000-0003-4051-3217")),
+    person("Craig", "Wenger", email = "craig.wenger@gmail.com",
+           role = "aut",
+           comment = c(ORCID = "0000-0002-7361-8456")),
+    person("Sarah", "Parker", email = "sarmae@live.unc.edu", role = "ctb"),
+    person("JP", "Flores", email = "jflores@unc.edu", role = "ctb"),
+    person("Erika", "Deoudes", email = "ed@erikadudes.com", role = "art"),
+    person("Michael", "Love", email = "milove@email.unc.edu", role = "ctb"),
+    person("Douglas H.", "Phanstiel", email = "douglas_phanstiel@med.unc.edu",
+           role = c("aut", "cph")))
 Description: 
     Coordinate-based genomic visualization package for R. It grants users
     the ability to programmatically produce complex, multi-paneled figures. Tailored for
     genomics, plotgardener allows users to visualize large complex genomic datasets and
     provides exquisite control over how plots are placed and arranged on a page. 
-Depends: R (>= 4.1.0)
+Depends: R (>= 4.2.0)
 License: MIT + file LICENSE
 URL: https://phanstiellab.github.io/plotgardener, https://github.com/PhanstielLab/plotgardener
 Encoding: UTF-8

R/annoDomains.R

@@ -17,7 +17,7 @@
 #' @param half Character value specifying which half of hic plots
 #' to annotate. Triangle Hi-C plots will always default to the entirety of
 #' the triangular plot. Default value is \code{half = "inherit"}. Options are:
-#' \itemize{
+#' \describe{
 #' \item{\code{"inherit"}: }{Domains will be annotated on the \code{half}
 #' inherited by the input Hi-C plot.}
 #' \item{\code{"both"}: }{Domains will be annotated on both halves of the

R/annoGenomeLabel.R

@@ -33,7 +33,7 @@
 #' and coordinate labels. Default value is \code{margin = unit(1, "mm")}.
 #' @param scale A character value indicating the scale of the coordinates
 #' along the genome label. Default value is \code{scale = "bp"}. Options are:
-#' \itemize{
+#' \describe{
 #' \item{\code{"bp"}: }{base pairs.}
 #' \item{\code{"Kb"}: }{kilobase pairs. 1 kilobase pair is equal to
 #' 1000 base pairs.}
@@ -51,7 +51,7 @@
 #' add genome label. Sequence information will not be displayed along a y-axis.
 #' Default value is \code{axis = "x"}.
 #' Options are:
-#' \itemize{
+#' \describe{
 #' \item{\code{"x"}: }{Genome label will be plotted along the x-axis.}
 #' \item{\code{"y"}: }{Genome label will be plotted along the y-axis.
 #' This is typically used for a square Hi-C plot made with

R/annoHeatmapLegend.R

@@ -23,7 +23,7 @@
 #' @param plot Heatmap-style plot object to add heatmap legend for.
 #' @param orientation A string specifying legend orientation.
 #' Default value is \code{orientation = "v"}. Options are:
-#' \itemize{
+#' \describe{
 #' \item{\code{"v"}: }{Vertical legend orientation.}
 #' \item{\code{"h"}: }{Horizontal legend orientation.}
 #' }

R/annoPixels.R

@@ -19,15 +19,15 @@
 #' positions.
 #' @param type Character value specifying type of annotation.
 #' Default value is \code{type = "box"}. Options are:
-#' \itemize{
+#' \describe{
 #' \item{\code{"box"}: }{Boxes are drawn around each pixel.}
 #' \item{\code{"circle"}: }{Circles are drawn around each pixel.}
 #' \item{\code{"arrow"}: }{Arrows are drawn pointing to each pixel.}
 #' }
 #' @param half Character value specifying which half of hic plots
 #' to annotate. Triangle Hi-C plots will always default to the entirety of
 #' the triangular plot. Default value is \code{half = "inherit"}. Options are:
-#' \itemize{
+#' \describe{
 #' \item{\code{"inherit"}: }{Pixels will be annotated on the \code{half}
 #' inherited by the input Hi-C plot.}
 #' \item{\code{"both"}: }{Pixels will be annotated on both halves of the

R/annoSegments.R

@@ -38,14 +38,14 @@
 #' Default value is \code{lty = 1}.
 #' @param lineend A character value specifying line end style.
 #' Default value is \code{lineend = "butt"}. Options are:
-#' \itemize{
-#' \item{\code{"round"}: Segment ends are rounded.}
-#' \item{\code{"butt"}: Segment ends end exactly where ended.}
-#' \item{\code{"square"}: Segment ends are squared.}
+#' \describe{
+#' \item{\code{"round"}: }{Segment ends are rounded.}
+#' \item{\code{"butt"}: }{Segment ends end exactly where ended.}
+#' \item{\code{"square"}: }{Segment ends are squared.}
 #' }
 #' @param linejoin A character value specifying line join style.
 #' Default value is \code{linejoin = "mitre"}. Options are:
-#' \itemize{
+#' \describe{
 #' \item{\code{"round"}: }{Line joins are rounded.}
 #' \item{\code{"mitre"}: }{Line joins are sharp corners.}
 #' \item{\code{"bevel"}: }{Line joins are flattened corners.}

R/annoXaxis.R

@@ -19,7 +19,7 @@
 #' If not logical, must be the same length as the \code{at} argument.
 #' @param main A logical value indicating whether to draw the x-axis at the
 #' bottom of the plot. Default value is \code{main = TRUE}. Options are:
-#' \itemize{
+#' \describe{
 #' \item{\code{TRUE}: }{x-axis is drawn at the bottom of the plot.}
 #' \item{\code{FALSE}: }{x-axis is drawn at the top of the plot.}
 #' }

R/annoYaxis.R

@@ -19,7 +19,7 @@
 #' If not logical, must be the same length as the \code{at} argument.
 #' @param main A logical value indicating whether to draw the y-axis at
 #' the left of the plot. Default value is \code{main = TRUE}. Options are:
-#' \itemize{
+#' \describe{
 #' \item{\code{TRUE}: }{y-axis is drawn at the left of the plot.}
 #' \item{\code{FALSE}: }{y-axis is drawn at the right of the plot.}
 #' }

R/plotGenomeLabel.R

@@ -41,7 +41,7 @@
 #' and coordinate labels. Default value is \code{margin = unit(1, "mm")},
 #' @param scale A character value indicating the scale of the coordinates
 #' along the genome label. Default value is \code{scale = "bp"}. Options are:
-#' \itemize{
+#' \describe{
 #' \item{\code{"bp"}: }{base pairs.}
 #' \item{\code{"Kb"}: }{kilobase pairs. 1 kilobase pair is equal to
 #' 1000 base pairs.}
@@ -59,7 +59,7 @@
 #' add genome label. Sequence information will not be displayed along a y-axis.
 #' Default value is \code{axis = "x"}.
 #' Options are:
-#' \itemize{
+#' \describe{
 #' \item{\code{"x"}: }{Genome label will be plotted along the x-axis.}
 #' \item{\code{"y"}: }{Genome label will be plotted along the y-axis.
 #' This is typically used for a square Hi-C plot made with

R/plotHicRectangle.R

@@ -42,7 +42,7 @@
 #' @param matrix Character value indicating the type of matrix to output for 
 #' .hic files.
 #' Default value is \code{matrix = "observed"}. Options are:
-#' \itemize{
+#' \describe{
 #' \item{\code{"observed"}: }{Observed counts.}
 #' \item{\code{"oe"}: }{Observed/expected counts.}
 #' \item{\code{"log2oe"}: }{Log2 transformed observed/expected counts.}

R/plotHicSquare.R

@@ -45,7 +45,7 @@
 #' @param matrix Character value indicating the type of matrix to output for
 #' .hic files.
 #' Default value is \code{matrix = "observed"}. Options are:
-#' \itemize{
+#' \describe{
 #' \item{\code{"observed"}: }{Observed counts.}
 #' \item{\code{"oe"}: }{Observed/expected counts.}
 #' \item{\code{"log2oe"}: }{Log2 transformed observed/expected counts.}
@@ -74,7 +74,7 @@
 #' or \code{"bottom"}. For off-diagonal or interchromosomal plotting,
 #' options are \code{"top"} or \code{"bottom"}.
 #' Default value is \code{half = "both"}.
-#' \itemize{
+#' \describe{
 #' \item{\code{"both"}: }{Both diagonal halves.}
 #' \item{\code{"top"}: }{Half above the diagonal.}
 #' \item{\code{"bottom"}: }{Half below the diagonal.}

R/plotHicTriangle.R

@@ -41,7 +41,7 @@
 #' @param matrix Character value indicating the type of matrix to output for
 #' .hic files.
 #' Default value is \code{matrix = "observed"}. Options are:
-#' \itemize{
+#' \describe{
 #' \item{\code{"observed"}: }{Observed counts.}
 #' \item{\code{"oe"}: }{Observed/expected counts.}
 #' \item{\code{"log2oe"}: }{Log2 transformed observed/expected counts.}

R/plotIdeogram.R

@@ -28,7 +28,7 @@
 #' @param orientation Character value indicating the orientation
 #' of the ideogram. Default value is \code{orientation = "h"}.
 #' Options are:
-#' \itemize{
+#' \describe{
 #' \item{\code{"v"}: }{Vertical ideogram orientation.}
 #' \item{\code{"h"}: }{Horizontal ideogram orientation.}
 #' }

R/plotLegend.R

@@ -29,7 +29,7 @@
 #' @param lty The line types for lines appearing in the legend.
 #' @param orientation A string specifying legend orientation.
 #' Default value is \code{orientation = "v"}. Options are:
-#' \itemize{
+#' \describe{
 #' \item{\code{"v"}: }{Vertical legend orientation.}
 #' \item{\code{"h"}: }{Horizontal legend orientation.}
 #' }

R/plotManhattan.R

@@ -36,7 +36,7 @@
 #' @param data Data to be plotted, as a character value specifying a
 #' file path of GWAS data, a dataframe, or a \link[GenomicRanges]{GRanges}
 #' object. Each of these data types must have the following columns:
-#' \itemize{
+#' \describe{
 #' \item{\code{"chrom"}: }{Chromosome names. This column must be a character.}
 #' \item{\code{"pos"}: }{Chromosomal position. This column must be
 #' an integer or numeric.}

R/plotMultiSignal.R

@@ -76,7 +76,7 @@
 #' Default value is \code{baseline.lwd = 1}.
 #' @param orientation A string specifying signal track orientations.
 #' Default value is \code{orientation = "h"}. Options are:
-#' \itemize{
+#' \describe{
 #' \item{\code{"v"}: }{Vertical signal track orientations, where signal tracks
 #' will be stacked from left to right.}
 #' \item{\code{"h"}: }{Horizontal signal track orientations, where signal tracks

R/plotPairs.R

@@ -43,7 +43,7 @@
 #' \link[plotgardener]{colorby} object specifying the color of the lines
 #' outlining paired range elements. Default value is \code{linecolor = NA}.
 #' Special options include:
-#' \itemize{
+#' \describe{
 #' \item{\code{NA}: }{No line color.}
 #' \item{\code{"fill"}: }{Same color as \code{fill}.}
 #' }

R/plotPairsArches.R

@@ -42,7 +42,7 @@
 #' Default value is \code{assembly = "hg38"}.
 #' @param style Character value describing the style of arches.
 #' Default value is \code{style = "2D"}. Options are:
-#' \itemize{
+#' \describe{
 #' \item{\code{"2D"}: }{Arches will be drawn in a 2-dimensional style.}
 #' \item{\code{"3D"}: }{Arches will be drawn in a 3-dimensional style.}
 #' }
@@ -60,7 +60,7 @@
 #' \link[plotgardener]{colorby} object specifying the color of the lines
 #' outlining arches. Default value is \code{linecolor = NA}.
 #' Special options include:
-#' \itemize{
+#' \describe{
 #' \item{\code{NA}: }{No line color.}
 #' \item{\code{"fill"}: }{Same color as \code{fill}.}
 #' }

R/plotRanges.R

@@ -47,14 +47,14 @@
 #' \link[plotgardener]{colorby} object specifying the color of the lines
 #' outlining range elements. Default value is \code{linecolor = NA}.
 #' Special options include:
-#' \itemize{
+#' \describe{
 #' \item{\code{NA}: }{No line color.}
 #' \item{\code{"fill"}: }{Same color as \code{fill}.}
 #' } .
 #' @param order A character value specifying how to order pileup data
 #' before assigning rows. Default value is \code{order = "width"}. Options 
 #' include:
-#' \itemize{
+#' \describe{
 #' \item{\code{"width"}: }{Ordered by decreasing width of elements.}
 #' \item{\code{"random"}: }{Ordered randomly in each function call.}
 #' } .

R/plotSegments.R

@@ -43,14 +43,14 @@
 #' Default value is \code{lty = 1}.
 #' @param lineend A character value specifying line end style.
 #' Default value is \code{lineend = "butt"}. Options are:
-#' \itemize{
-#' \item{\code{"round"}: Segment ends are rounded.}
-#' \item{\code{"butt"}: Segment ends end exactly where ended.}
-#' \item{\code{"square"}: Segment ends are squared.}
+#' \describe{
+#' \item{\code{"round"}: }{Segment ends are rounded.}
+#' \item{\code{"butt"}: }{Segment ends end exactly where ended.}
+#' \item{\code{"square"}: }{Segment ends are squared.}
 #' }
 #' @param linejoin A character value specifying line join style.
 #' Default value is \code{linejoin = "mitre"}. Options are:
-#' \itemize{
+#' \describe{
 #' \item{\code{"round"}: }{Line joins are rounded.}
 #' \item{\code{"mitre"}: }{Line joins are sharp corners.}
 #' \item{\code{"bevel"}: }{Line joins are flattened corners.}

R/plotSignal.R

@@ -77,7 +77,7 @@
 #' Default value is \code{baseline.lwd = 1}.
 #' @param orientation A string specifying signal track orientation.
 #' Default value is \code{orientation = "h"}. Options are:
-#' \itemize{
+#' \describe{
 #' \item{\code{"v"}: }{Vertical signal track orientation.}
 #' \item{\code{"h"}: }{Horizontal signal track orientation.}
 #' }

R/plotTranscripts.R

@@ -69,7 +69,7 @@
 #' @param labels A character value describing the format of
 #' transcript text labels. Default value is \code{labels = "trancript"}.
 #' Options are:
-#' \itemize{
+#' \describe{
 #' \item{\code{NULL}: }{No labels.}
 #' \item{\code{"transcript"}: }{Transcript name labels.}
 #' \item{\code{"gene"}: }{Gene name labels.}

R/plotgardener.R

@@ -68,3 +68,5 @@
 #' @importFrom GenomeInfoDb keepStandardChromosomes
 #' @importFrom GenomicRanges makeGRangesFromDataFrame
 "_PACKAGE"
+
+utils::globalVariables(c("name", "width", "strand"))

R/readBigwig.R

@@ -16,7 +16,7 @@
 #' @param chromend Integer end position on chromosome.
 #' @param strand A character value specifying strand.
 #' Default value is \code{strand = "*"}. Options are:
-#' \itemize{
+#' \describe{
 #' \item{\code{"+"}: }{Plus strand.}
 #' \item{\code{"-"}: }{Minus strand.}
 #' \item{\code{"*"}: }{Plus and minus strands.}

R/readCool.R

@@ -1,8 +1,12 @@
 #' Check for .(m)cool file and contents
 #' @author Sarah Parker
-#' 
+#'
 #' @param file Path to .(m)cool file
-#' 
+#'
+#' @return A character string, either \code{".cool"} or \code{".mcool"},
+#'   indicating the file type. Aborts with an error if the file is not a
+#'   valid .(m)cool file.
+#'
 #' @importFrom glue glue glue_collapse
 #' @importFrom rlang abort
 #' @importFrom rhdf5 H5Fis_hdf5 h5ls
@@ -236,6 +240,9 @@ readCoolChroms <- function(file, resolution = NULL){
 #' @param file Path to .(m)cool file
 #' @param chromstart Chromstart of region
 #' @param chromend Chromend of region
+#'
+#' @return A numeric value specifying the automatically determined resolution
+#'   in base pairs.
 .coolAutoResolution <- function(file, chromstart, chromend){
 
     fileResolutions <- readCoolBpResolutions(file)
@@ -300,6 +307,9 @@ readCoolChroms <- function(file, resolution = NULL){
 #' @param file Path to .(m)cool file
 #' @param chrom Chromosome of region; can also be altchromosome
 #' @param resolution Resolution to read chromsome info from
+#'
+#' @return A list of length two containing the chromosome start position (1)
+#'   and the chromosome length.
 .coolRegion <- function(file, chrom, resolution){
 
     chromInfo <- readCoolChroms(file, resolution = resolution)
@@ -319,7 +329,10 @@ readCoolChroms <- function(file, resolution = NULL){
 #' @param end1bin Bin where end1 starts
 #' @param start2bin Bin for chr2 starts
 #' @param end2bin Bin for end2 starts
-#' 
+#'
+#' @return An integer vector of pixel indices corresponding to interactions
+#'   within the specified bin chunk, or \code{NA} if none are found.
+#'
 #' @importFrom rhdf5 h5read
 .pullBinChunks <- function(binChunk, file, bin_offsets, binChunkSize,
                            datasetPath, end1bin,
@@ -357,7 +370,10 @@ readCoolChroms <- function(file, resolution = NULL){
 #' @param altchromend User-inputted alt chromend.
 #' @param norm User-inputted normalization.
 #' @param resolution Resolution, either user-inputted or determined by 'auto'.
-#' 
+#'
+#' @return Called for side effects (input validation). Aborts with an
+#'   informative error if any inputs are invalid.
+#'
 #' @importFrom glue glue
 #' @importFrom rlang abort
 .checkCoolErrors <- function(file, chrom, chromstart, chromend, zrange,