ggspavis

[lmweber]

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[bioc-issue-bot]

Hi @lmweber

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: ggspavis
Version: 0.99.0
Title: Visualization functions for spatially resolved transcriptomics data
Description: Visualization functions for spatially resolved transcriptomics 
    datasets stored in SpatialExperiment format. Includes functions to create 
    several types of plots for data from from spot-based (e.g. 10x Genomics 
    Visium) and molecule-based (e.g. seqFISH) technological platforms.
Authors@R: c(
    person("Lukas M.", "Weber", email = "lukas.weber.edu@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-3282-1730")), 
    person("Helena L.", "Crowell", email = "helena.crowell@uzh.ch", role = c("aut"), comment = c(ORCID = "0000-0002-4801-1767")))
URL: https://github.com/lmweber/ggspavis
BugReports: https://github.com/lmweber/ggspavis/issues
License: MIT + file LICENSE
biocViews:
    SingleCell, 
    Transcriptomics
Imports:
    SpatialExperiment, 
    SingleCellExperiment, 
    SummarizedExperiment, 
    ggplot2, 
    ggside, 
    grid, 
    methods, 
    stats
VignetteBuilder: knitr
Suggests:
    BiocStyle, 
    rmarkdown, 
    knitr, 
    STexampleData
RoxygenNote: 7.1.1

[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 Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be 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/ggspavis 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: c2a56309c1f13b188ba3ef5359326b4259bbad7c

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be 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/ggspavis 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: f5ec57f001fc5a7d1164b88c7b860de6e7fa4024

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be 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/ggspavis 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: a29e608ba8e4af8a8b4da9040f032909f9cc0292

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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

Please see the build report for more details. This link will be 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/ggspavis to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[LiNk-NY]

Hi Lukas, @lmweber Thank you for your submission. Please see the review below. Feel free to ask any questions. Best regards, Marcel

---

ggspavis #2220

DESCRIPTION

• Looks good.
• Consider adding ggplot2 to the Depends field given the number of imported functions in the NAMESPACE.
• (Minor) Format the Authors@R field to wrap the text to less than 80 column width.

NAMESPACE

• There are only a handful of exported functions. Looks good.

vignettes/

• Consider restricting the text to 80 column width. It makes it easier to review and maintain IMO.
• Nice visuals and examples. The vignette is concise.

R

• Make sure you are using match.arg in plotDimRed to ensure that your code is robust to inputs outside of c("UMAP", "PCA").

• Plotting the example in plotDimRed does not use the default palette. It looks like it depends on annotate being present, otherwise the palette input does not work.

• Consider using .get_pal in plotDimRed as well.

• Add some checks to inputs (e.g., molecule in plotMolecules) to ensure robustness

• Avoid redundancy by using a character input for in_tissue and using df[[in_tissue]] within the code. The default argument value can be "in_tissue" or even rename the argument to tissue_column.

• Minor: Consider using identical(palette, "libd_layer_colors") etc. within your if conditions.

• Minor: Consider using cbind.data.frame instead of as.data.frame(cbind(...)) in plotQC.

/

• Update section in README.md to reflect the use of BiocManager for installation (after acceptance).

tests

• Consider adding unit tests to make the code more robust.

[lmweber]

Thanks Marcel @LiNk-NY ! Will work through these comments and push some updates.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 740c2e82d084f3d589e7bfdebbdf2d2a65da5daf

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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

Please see the build report for more details. This link will be 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/ggspavis to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[lmweber]

Hi Marcel @LiNk-NY - I have pushed the following updates. Thank you!

---

DESCRIPTION

Looks good.

Consider adding ggplot2 to the Depends field given the number of imported functions in the NAMESPACE.

Done

(Minor) Format the Authors@R field to wrap the text to less than 80 column width.

Done

NAMESPACE

There are only a handful of exported functions. Looks good.

vignettes/

Consider restricting the text to 80 column width. It makes it easier to review and maintain IMO.

I prefer to leave this with the longer lines of text, since for me this is easier to maintain. I use RStudio as my IDE, which wraps the text, so I find it easier to rewrite a paragraph if it is all in a single line. I use the 80 character column width in my code blocks.

Nice visuals and examples. The vignette is concise.

R

Make sure you are using match.arg in plotDimRed to ensure that your code is robust to inputs outside of c("UMAP", "PCA").

Done (in plotDimRed and other functions)

Plotting the example in plotDimRed does not use the default palette. It looks like it depends on annotate being present, otherwise the palette input does not work.

Done. I replaced the example with some longer code that generates a real plot.

Consider using .get_pal in plotDimRed as well.

Done (in plotDimRed and other functions)

Add some checks to inputs (e.g., molecule in plotMolecules) to ensure robustness

Done (in plotMolecules and other functions)

Avoid redundancy by using a character input for in_tissue and using df[[in_tissue]] within the code. The default argument value can be "in_tissue" or even rename the argument to tissue_column.

Done

Minor: Consider using identical(palette, "libd_layer_colors") etc. within your if conditions.

Now using .get_pal() instead, so I have removed these if statements.

Minor: Consider using cbind.data.frame instead of as.data.frame(cbind(...)) in plotQC.

Done (in plotQC and other functions)

/

Update section in README.md to reflect the use of BiocManager for installation (after acceptance).

Will update after acceptance.

tests

Consider adding unit tests to make the code more robust.

Done

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 840e1737518e49b230fc735fc65a807fe6587970

[lmweber]

I also added uwot to Suggests in dependencies after noticing this was giving an error in my GitHub Actions build, due to the new example code that depends on uwot.

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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

Please see the build report for more details. This link will be 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/ggspavis to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Dear Package contributor,

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

Your package has been built on Linux, Mac, and Windows.

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

Please see the build report for more details. This link will be 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/ggspavis to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[LiNk-NY]

Hi Lukas, @lmweber

Thank you for making those changes. They look great! Thank you for your contribution to Bioconductor.

Best regards, Marcel

[bioc-issue-bot]

Your package has been accepted. It will be added to the Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

Reviewers for Bioconductor packages are volunteers from the Bioconductor community. If you are interested in becoming a Bioconductor package reviewer, please see Reviewers Expectations.

[lmweber]

Great, thanks Marcel @LiNk-NY !

[vjcitn]

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(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("ggspavis"). The package 'landing page' will be created at

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