BioCartaImage

[jokergoo]

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[bioc-issue-bot]

Hi @jokergoo

Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: BioCartaImage
Type: Package
Title: BioCarta Pathway Images
Version: 0.99.0
Date: 2023-09-22
Authors@R: person("Zuguang", "Gu", email = "z.gu@dkfz.de", role = c("aut", "cre"),
        comment = c('ORCID'="0000-0002-7395-8709"))
Depends: R (>= 4.2.0)
Imports: magick, grid, stats, grDevices, utils
Suggests: testthat, knitr
biocViews: Software, Pathways, BioCarta, Visualization
Description: The core functionality of the package is to provide coordinates of genes
    on the pathway image and to provide methods to add self-defined graphics to the genes of interest.
VignetteBuilder: knitr
URL: https://github.com/jokergoo/BioCartaImage
License: MIT + file LICENSE
NeedsCompilation: no
RoxygenNote: 7.2.3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)

[lshep]

We do not allow data to be downloaded from github. IMAGE_BASE_URL = "https://jokergoo.github.io/BioCartaImage/image/" Please upload data to a trusted server like zenodo, AWS S3 buckets, Microsoft Azure Data Lakes, etc. or minimally an institutional level server. Un-trusted sites like personal github and dropbox are not allowed.

[jokergoo]

I found the files are also hosted on https://data.broadinstitute.org/gsea-msigdb/msigdb/biocarta/human/. I will use it instead of GitHub.

[lshep]

Yes updating to grab directly from there will be better. Please let us know when the code has been updated and we will look over again.

[jokergoo]

It has already been updated.

https://github.com/jokergoo/BioCartaImage/blob/fe4abf60658f630d06f99768bd8ac09a682a14a8/R/biocarta.R#L86

[bioc-issue-bot]

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[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): BioCartaImage_0.99.1.tar.gz macOS 12.6.5 Monterey: BioCartaImage_0.99.1.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/BioCartaImage to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

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[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: fffb3a81ce10a960867c8f2aec9a17a445743d5d

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): BioCartaImage_0.99.2.tar.gz macOS 12.6.5 Monterey: BioCartaImage_0.99.2.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/BioCartaImage to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[HelenaLC]

other

• [ ] in the README, please add Bioconductor installation instructions using BiocManager::install()

• [ ] BiocCheck() NOTE: update R version dependency from 4.2.0 to 4.3.0 (Bioc 3.18 will not be installable with anything less) in the DESCRIPTION

• [ ] in the DESCRIPTION, consider adding a BugReports: field referencing https://github.com/jokergoo/BioCartaImage/issues

code/

• [ ] appreciate there's testing (!), though coverage could be improved (~66% with 6 hits per line according to devtools::test_coverage())

• [ ] BiocCheck() NOTE: avoid using = for assignment and use <- instead

• [ ] nothing 'wrong', but validity of character string values such as in biocarta.R lines 471+ is nicely done with match.arg() (see below); this has the pros that valid options are directly displayed in the function documentation, and an automated (informative) error is thrown upon violation (*note that valid choices can also be checked inside the function only, and needn't be in the function definition, if that's preferred)

pos_by_polygon <- function(x, y, where=c("left", "right", "top",
    "bottom","topleft", "topright", "bottomleft", "bottomright")) {
    where <- match.arg(where)
}

• [ ] again no issue, just wanted to point out that biocarta.R lines 476+ could be nicely (I think) written using switch(), i.e.:

switch(where,
    left=c(min(x), mean(y)),
    right=c(max(x), mean(y)),
    ...)

• [ ] line 55: consider defining n <- length(unique(BC2ENTREZ$ENTREZ[BC2ENTREZ$BCID %in% x$genes])) for clarity, and as to not go over the recommended 80-character line limit

• [ ] lines 448+ could be written more succinctly as coords[c(1, 1, 3, 3, 1)]

documentation

• [ ] function documentation is very minimal for various functions (e.g., all_pathways, genes_in_pathway, ...); could you expand these a little? e.g., rather than stating that "a vector of pathway IDs" is returned, also write what type of pathways these are/where they come from, and perhaps list the corresponding resource/reference?

• [ ] consider adding a package help/.man package (BioCartaImage), e.g., briefly summarizing the package's key functionality, hyperlinking functions etc.

• [ ] please provide source information/a description of how the data/ were generated; I think the corresponding scripts are already correctly placed in inst/scripts/

vignettes/

• [ ] we encourage the use of r BiocStyle::Biocpkg("BiocStyle") for formatting with html_document as rendering target, e.g.:

output:
  BiocStyle::html_document:
    toc: true
    toc_depth: 2

• [ ] could you clarify: the print method of biocarta_pathway object p says "35 nodes, 16 genes", however, I am getting length(unique(p$genes)) -> 13? I see that the show method accessed the genes in the corresponding pathway, however, I find this confusing confusing still; perhaps the show method could display both (what's in the pathway and what's in the object, if that makes sense?)

• [ ] the output of str(p) is fairly messy and hard to interpret (especially for less programmatically inclined users); instead, might it be worth considering describing relevant elements (what's in $genes, coords, etc.)?

• [ ] the grid.pathway() outputs produce a lot of white space; would it be possible to somehow 'prettify' this, e.g., using code chunk options/adjusting certain parameters? (*I am not referring to the viewport, but rather the space introduced by knitr defaults)

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: d1857f4992284b724f3aad3676f5e2ecd5152496

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): BioCartaImage_0.99.4.tar.gz macOS 12.6.5 Monterey: BioCartaImage_0.99.4.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/BioCartaImage to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[jokergoo]

Thank you for your time and your comments!

other

• [x] in the README, please add Bioconductor installation instructions using BiocManager::install()
• [x] BiocCheck() NOTE: update R version dependency from 4.2.0 to 4.3.0 (Bioc 3.18 will not be installable with anything less) in the DESCRIPTION
• [x] in the DESCRIPTION, consider adding a BugReports: field referencing https://github.com/jokergoo/BioCartaImage/issues

code/

• [x] appreciate there's testing (!), though coverage could be improved (~66% with 6 hits per line according to devtools::test_coverage())

I have tried my best to improve the code coverage. Now it is 83%.

• [ ] BiocCheck() NOTE: avoid using = for assignment and use <- instead

I prefer to use = for assignment.

• [x] nothing 'wrong', but validity of character string values such as in biocarta.R lines 471+ is nicely done with match.arg() (see below); this has the pros that valid options are directly displayed in the function documentation, and an automated (informative) error is thrown upon violation (*note that valid choices can also be checked inside the function only, and needn't be in the function definition, if that's preferred)

pos_by_polygon <- function(x, y, where=c("left", "right", "top",
    "bottom","topleft", "topright", "bottomleft", "bottomright")) {
    where <- match.arg(where)
}

• [x] again no issue, just wanted to point out that biocarta.R lines 476+ could be nicely (I think) written using switch(), i.e.:

switch(where,
    left=c(min(x), mean(y)),
    right=c(max(x), mean(y)),
    ...)

• [x] line 55: consider defining n <- length(unique(BC2ENTREZ$ENTREZ[BC2ENTREZ$BCID %in% x$genes])) for clarity, and as to not go over the recommended 80-character line limit
• [x] lines 448+ could be written more succinctly as coords[c(1, 1, 3, 3, 1)]

documentation

• [x] function documentation is very minimal for various functions (e.g., all_pathways, genes_in_pathway, ...); could you expand these a little? e.g., rather than stating that "a vector of pathway IDs" is returned, also write what type of pathways these are/where they come from, and perhaps list the corresponding resource/reference?

I have improved the function documentation as well as the vignette.

• [ ] consider adding a package help/.man package (BioCartaImage), e.g., briefly summarizing the package's key functionality, hyperlinking functions etc.

I think since all Bioc packages have vignettes (unlike CRAN packages), for me the first step is always to go to the vignettes. BioCartaImage is a small package, if I create a package-level rd file, it basically just copies text from the vignette, which I think for this package is not necessary.

• [x] please provide source information/a description of how the data/ were generated; I think the corresponding scripts are already correctly placed in inst/scripts/

It is added in the vignette.

vignettes/

• [x] we encourage the use of r BiocStyle::Biocpkg("BiocStyle") for formatting with html_document as rendering target, e.g.:

output:
  BiocStyle::html_document:
    toc: true
    toc_depth: 2

• [x] could you clarify: the print method of biocarta_pathway object p says "35 nodes, 16 genes", however, I am getting length(unique(p$genes)) -13? I see that the show method accessed the genes in the corresponding pathway, however, I find this confusing confusing still; perhaps the show method could display both (what's in the pathway and what's in the object, if that makes sense?)

It was indeed confusing. It should be not called "genes" because p$genes are actually nodes or proteins in the pathway where the mapping to "real genes" is not always one-to-one. In the new version, I have changed the name "genes" to "bc" (bc means internal biocarta ID for nodes/proteins). In this way, length(p$bc) is the number of nodes in the pathway. Note here I did not apply unique() because the term "nodes" is under the context of a network and multiple existences of the same node contribute to the topology of the network. Whereas when I measure the number of genes, I take the unique number of genes that are mapped to the pathway. Also explained in the vignette.

• [x] the output of str(p) is fairly messy and hard to interpret (especially for less programmatically inclined users); instead, might it be worth considering describing relevant elements (what's in $genes, coords, etc.)?

Now it is explained in the documentation of get_pathway() as well as in the vignette.

• [x] the grid.pathway() outputs produce a lot of white space; would it be possible to somehow 'prettify' this, e.g., using code chunk options/adjusting certain parameters? (*I am not referring to the viewport, but rather the space introduced by knitr defaults)

This is on purpose. grid.pathway() is not for making a high-level plot. It is for providing a graphic component for a larger plot, like grid.points(). There are some examples where you see a lot of white spaces around. That is for demonstrating drawing the pathway in a sub-viewport which might be 1/4 of the parent viewport.

In the new version, I explicitly added the borders of the whole figure to show the white areas are parts of the figures that are demonstrated in the examples.

[HelenaLC]

Thanks for the prompt response and addressing things! Couple more comments, with 1-2 being majorish, the other briefly clarifying earlier comments...

• Regarding data/ source information ("It is added in the vignette."), this is not sufficient. Please also document the data/ in a way that is programmatically accessible (via ?). Also, I don't find it intuitive where to find the corresponding documentation. E.g., searching for .RData object BC2ENRTEZ, PATHWAY2BC etc. I don't get any matches in the vignette. The data is already being briefly described in terms for data structure (dimensions and variables) - what is missing is provenance information.

• Some of the documentation I mentioned is still too minimal for my liking... E.g., it would be nice if ?genes_in_pathway and ?get_pathway_image (or any other function having a pathway argument) included how valid pathways from different resources are retrieved; otherwise, how would one know (without typos or going online) what are valid values for pathway? To link to useful information across .man pages, hyperlinks via \code{\link{...}} or the #' @seealso roxygen tag might be useful, as you are already doing in other help pages.

• Similar to the above, the point of a ?BiocCartaImage help page is not to replace the vignette, but to have users be able to have programmatic access (from within R) to a brief summary of the package, quick-links to key functions etc. - it is not a requirement, so you're call, just wanted to clarify why we recommend this :)

• Regarding = vs. <-: Just to point out that this has less to do with what is "preferred", i.e., it is not a difference in syntax but semantics. Specifically, these operators can - in certain contexts - behave differently (!); hence we recommend refraining from using = for assignment in all cases, although this is only a NOTE (for now).

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 112aefbaeb44cd59880b04074f4892afcc925766

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Bioconductor Build System: macOS 12.6.5 Monterey: BioCartaImage_0.99.5.tar.gz Linux (Ubuntu 22.04.2 LTS): BioCartaImage_0.99.5.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/BioCartaImage to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: daee920ce52cd3ed0293ca761204feb6dff811b6

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Build System.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

The following are build products from R CMD build on the Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): BioCartaImage_0.99.6.tar.gz macOS 12.6.5 Monterey: BioCartaImage_0.99.6.tar.gz

Links above active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/BioCartaImage to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[jokergoo]

Thanks for your reply!

Regarding data/ source information ("It is added in the vignette."), this is not sufficient. Please also document the data/ in a way that is programmatically accessible (via ?). Also, I don't find it intuitive where to find the corresponding documentation. E.g., searching for .RData object BC2ENRTEZ, PATHWAY2BC etc. I don't get any matches in the vignette. The data is already being briefly described in terms for data structure (dimensions and variables) - what is missing is provenance information.

I have added more text describing the source of these datasets in the documentations.

"searching for .RData object BC2ENRTEZ, PATHWAY2BC etc. I don't get any matches in the vignette". They should be able to be visited by ?BC2ENRTEZ.

Some of the documentation I mentioned is still too minimal for my liking... E.g., it would be nice if ?genes_in_pathway and ?get_pathway_image (or any other function having a pathway argument) included how valid pathways from different resources are retrieved; otherwise, how would one know (without typos or going online) what are valid values for pathway? To link to useful information across .man pages, hyperlinks via \code{\link{...}} or the #' @seealso roxygen tag might be useful, as you are already doing in other help pages.

I added more text describing the valid format of pathways. I have checked all functions that accept pathways as input.

Similar to the above, the point of a ?BiocCartaImage help page is not to replace the vignette, but to have users be able to have programmatic access (from within R) to a brief summary of the package, quick-links to key functions etc. - it is not a requirement, so you're call, just wanted to clarify why we recommend this :)

Yes, I agree that is useful and necessary. I have added it in the package.

Regarding = vs. <-: Just to point out that this has less to do with what is "preferred", i.e., it is not a difference in syntax but semantics. Specifically, these operators can - in certain contexts - behave differently (!); hence we recommend refraining from using = for assignment in all cases, although this is only a NOTE (for now).

I know the difference between "=" and "<-" very clearly. But personal for me as an old programmer, I don't see the difference is big enough for me to change my coding style.

[HelenaLC]

Thanks for the updates, it's all looking well. However, the package .man pages is currently not directly found (at least not how I tried viewing it at first, i.e., ?BioCartaImage fails). You should add an @aliases tag to fix this, specifically:

# in package.R:
#' @aliases BioCartaImage

I'll accept now as a package-help page is not a requirement. But would suggest adding this, since you already spent time putting together that piece of documentation.

[bioc-issue-bot]

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[bioc-issue-bot]

cannot build unless issue is open and has the 'pre-review' label or '2. review in progress' label, or is closed and has the 'TESTING' label.

[bioc-issue-bot]

cannot build unless issue is open and has the 'pre-review' label or '2. review in progress' label, or is closed and has the 'TESTING' label.

[jokergoo]

Thanks! I will add it.

[lshep]

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