diff --git a/DESCRIPTION b/DESCRIPTION index b2563e9..f3c53f5 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -8,14 +8,13 @@ Authors@R: c( comment = c(ORCID = "0000-0002-3913-153X")) ) Maintainer: Yabing Song -Description: The goal of 'ggcoverage' is to visualize coverage tracks from - genomics, transcriptomics or proteomics data. It contains functions to - load data from BAM, BigWig, BedGraph, txt, or xlsx files, create - genome/protein coverage plots, and add various annotations including - base and amino acid composition, GC content, copy number variation - (CNV), genes, transcripts, ideograms, peak highlights, HiC contact - maps, contact links and protein features. It is based on and - integrates well with 'ggplot2'. +Description: Visualize coverage tracks from genomics, transcriptomics + or proteomics data. The package contains functions to load data from 'BAM', + 'BigWig', 'BedGraph', 'txt', or 'xlsx' files, create genome/protein coverage + plots, and add various annotations including base and amino acid + composition, GC content, copy number variation (CNV), genes, transcripts, + ideograms, peak highlights, HiC contact maps, contact links and protein + features. It is based on and integrates well with 'ggplot2'. License: MIT + file LICENSE URL: https://showteeth.github.io/ggcoverage/, https://github.com/showteeth/ggcoverage @@ -51,6 +50,7 @@ Suggests: HiCBricks, htmltools, knitr, + openxlsx, rmarkdown VignetteBuilder: knitr diff --git a/README.Rmd b/README.Rmd index 0f0b77f..84d64ff 100644 --- a/README.Rmd +++ b/README.Rmd @@ -446,10 +446,8 @@ THe default color scheme for base annotation is `Clustal-style`, more popular co nuc_color <- c( "A" = "#ff2b08", "C" = "#009aff", "G" = "#ffb507", "T" = "#00bc0d" ) -opar <- graphics::par() # create plot -graphics::par(mar = c(1, 5, 1, 1)) graphics::image( seq_along(nuc_color), 1, @@ -468,9 +466,6 @@ graphics::mtext( las = 1, side = 2 ) - -# reset par default -graphics::par(opar) ``` Default color scheme for amino acid annotation is from [Residual colours: a proposal for aminochromography](https://pubmed.ncbi.nlm.nih.gov/9342138/): @@ -486,7 +481,6 @@ aa_color <- c( " " = "#FFFFFF" ) -graphics::par(mar = c(1, 5, 1, 1)) graphics::image( 1:5, 1:5, @@ -506,9 +500,6 @@ graphics::mtext( las = 1, side = 2 ) - -# reset par default -graphics::par(opar) ``` #### Add base and amino acid annotation diff --git a/README.md b/README.md index b1af77a..bb174a4 100644 --- a/README.md +++ b/README.md @@ -626,10 +626,8 @@ popular color schemes are available nuc_color <- c( "A" = "#ff2b08", "C" = "#009aff", "G" = "#ffb507", "T" = "#00bc0d" ) -opar <- graphics::par() # create plot -graphics::par(mar = c(1, 5, 1, 1)) graphics::image( seq_along(nuc_color), 1, @@ -652,12 +650,6 @@ graphics::mtext( -``` r - -# reset par default -graphics::par(opar) -``` - Default color scheme for amino acid annotation is from [Residual colours: a proposal for aminochromography](https://pubmed.ncbi.nlm.nih.gov/9342138/): @@ -673,7 +665,6 @@ aa_color <- c( " " = "#FFFFFF" ) -graphics::par(mar = c(1, 5, 1, 1)) graphics::image( 1:5, 1:5, @@ -697,12 +688,6 @@ graphics::mtext( -``` r - -# reset par default -graphics::par(opar) -``` - #### Add base and amino acid annotation **Use twill to mark position with SNV**: diff --git a/cran-comments.md b/cran-comments.md index 4576a09..de9d90e 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,6 +1,20 @@ # Resubmission -Update for current submission: +This package has been submitted previously (2023, v0.7.1) and was removed +from CRAN due to several issues, which have been addressed now. + +## Issues + +### Update for current submission: + +- fixed DESCRIPTION abstract, added quotation marks for package names etc +- examples that are running >5 sec were wrapped in `/donttest{}` instead of `/dontrun{}` +- example in `ggcoverage.Rd` does not contain out-commented code as stated by the reviewer +- changing of graphical parameters using `par(mfrow=c(2,2))` were removed from vignette +- however the package does not contain any `par()` statement in any of the + functions (supposedly `R/geom_base.R`) as stated by the reviewer + +### Previously fixed issues - We have substantially removed the size of test files for the examples, reducing overall package size from ~30 Mb to only ~6 Mb. A further reduction @@ -13,14 +27,6 @@ on the test environment -- this package never exceeds the threshold when tested locally on a 3 year old average laptop, or in 3 different github actions workflows, but regularly fails on the CRAN server. -Background information: - -This package has been submitted previously (2023, v0.7.1) and was removed from -CRAN due to several issues. In the mean time many functions were re-factored, -more than 10 dependencies were removed to make the package lighter, and other -problems regarding documentation and style were fixed. Current version 1.4.0 -now builds fine on the tested platforms. - ## Test environments ### Local diff --git a/vignettes/ggcoverage.Rmd b/vignettes/ggcoverage.Rmd index 0e62a25..4120bc7 100644 --- a/vignettes/ggcoverage.Rmd +++ b/vignettes/ggcoverage.Rmd @@ -475,10 +475,8 @@ THe default color scheme for base annotation is `Clustal-style`, more popular co nuc_color <- c( "A" = "#ff2b08", "C" = "#009aff", "G" = "#ffb507", "T" = "#00bc0d" ) -opar <- graphics::par() # create plot -graphics::par(mar = c(1, 5, 1, 1)) graphics::image( seq_along(nuc_color), 1, @@ -497,9 +495,6 @@ graphics::mtext( las = 1, side = 2 ) - -# reset par default -graphics::par(opar) ``` Default color scheme for amino acid annotation is from [Residual colours: a proposal for aminochromography](https://pubmed.ncbi.nlm.nih.gov/9342138/): @@ -515,7 +510,6 @@ aa_color <- c( " " = "#FFFFFF" ) -graphics::par(mar = c(1, 5, 1, 1)) graphics::image( 1:5, 1:5, @@ -535,9 +529,6 @@ graphics::mtext( las = 1, side = 2 ) - -# reset par default -graphics::par(opar) ``` #### Add base and amino acid annotation