tomoda

[liuwd15]

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• Repository: https://github.com/liuwd15/tomoda

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[bioc-issue-bot]

Hi @liuwd15

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: tomoda
Title: Tomo-seq data analysis
Version: 0.99.0
Authors@R: 
    person(given = "Wendao",
 family = "Liu",
 role = c("aut", "cre"),
 email = "liuwd15@tsinghua.org.cn",
           comment = c(ORCID = "0000-0002-5124-9338"))
Description: This package provides many easy-to-use methods to analyze and 
    visualize tomo-seq data. The main purpose of the package is to find zones
    with similar transcriptional profiles and spatially expressed genes in a 
    tomo-seq sample. Several visulization functions are available to create
    high quality and easy-to-modify plots.
Depends: R (>= 4.0.0)
Imports:
    methods,
    stats,
    grDevices,
    reshape2,
    Rtsne,
    umap,
    colorRamps,
    ggplot2,
    ggrepel,
    SummarizedExperiment
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
Suggests: 
    knitr,
    rmarkdown,
    BiocStyle,
    testthat
URL: https://github.com/liuwd15/tomoda
BugReports: https://github.com/liuwd15/tomoda/issues
biocViews: 
    GeneExpression, 
    Sequencing,
    RNASeq, 
    Transcriptomics,
    Clustering, 
    Visualization
VignetteBuilder: knitr

[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.

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/tomoda to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[LiNk-NY]

Hi Wendao Liu, @liuwd15

Thank you for your submission to Bioconductor. Please see the review below. Feel free to post any questions or comments below.

Best regards, Marcel

---

tomoda #1635

DESCRIPTION

• Briefly describe the tomo-seq technology and possibly even provide a reference.

NAMESPACE

• (optional) An unwritten convention is to use capital case function names for constructor functions for classes (e.g., SummarizedExperiment()). Otherwise, use lower case for 'plain' functions.
• The names of some functions are quite general and can cause confusion for your users (e.g., base::scale vs Scale and stats::kmeans vs KMeans). Please add a more descriptive name to your functions or consider renaming them.
• The number of exports looks reasonable though I'd be careful with function names that differ only by case.

vignettes

• Consider limiting your lines to the 80 column width in the vignette. It makes it easier for the reviewer to read and potentially for the maintainer to update.
• Use r BiocStyle::Biocpkg('tomoda') when accepted.
• Why not use a SummarizedExperiment to represent the example dataset (zh.data)
• Should Normalize and Scale operations be part of your CreateTomo function?
• Use color-blind friendly default colors for the heatmaps.
• Remove the .gitignore file in the vignettes folder (.R and .html files do not belong in the directory).

R

• CreateTomo should support both matrix and SummarizedExperiment inputs.
• You can also have a normalize / scale argument in the CreateTomo function.
• Consider renaming CreateTomo to something like checkTomo as 'Tomo' is not really a class or subclass of SummarizedExperiment.
• Add more details in the documentation to what operations are performed on the data as part of the CreateTomo function.
• Given that SummarizedExperiment is the main data representation. The GetMatrix function is repeated code for assay(se, i = "counts") and should be removed. The documentation should inform users to use the assay function to extract a matrix.
• Avoid using cat and use message instead to notify the user.
• HClust and KMeans seem to be thin wrappers for hclust and kmeans and consider including the convenience functions inside the main CreateTomo, if at all.
• Avoid hardcoding the assay name in FindPeakGene (assays(object)$scaled). Allow the user to input the scaled assay name (scaled) using an argument. This applies to other functions that use assays(object)$scaled etc.
• Use assay rather than assays when extracting one
• Use the allocate and fill strategy in FindPeakGene for loop when nperm > 0.

README.md

• Update the BiocManger::install code chunk

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: b44e45d4a8ccab5c0cadddf761c954d0be2a2be0

[liuwd15]

Hi Marcel @LiNk-NY, Thanks for your comments. I have updated the package and here are my responses to your comments. I followed most of your comments but left a few unchanged. The reasons are explained below.

DESCRIPTION

• Description and reference are added.

NAMESPACE

• Functions are renamed such that they follow the convention (starts with lower cases) and differ from other functions.

vignettes

• The vignette is now 80 column-wide.

• Now r BiocStyle::Biocpkg('tomoda') is used.

• In my opinion, most users will start with a read count matrix rather than a SummarizedExperiment object. The example matrix is useful as I show how to create the SummarizedExperiment object from a read count matrix. If the dataset is saved as a SummarizedExperiment object, users may not understand how to prepare their data. Therefore I believe saving the example dataset as matrix is reasonable.

• Normalization and scaling are now added into createTomo.

• Color-blind friendly default colors from RColorBrewer are used for heatmaps now.

• .gitignore in this directory is removed.

R

• createTomo now supports matrix and SummarizedExperiment inputs by using S4 generics and methods.

• Normalization and scaling are now added into createTomo.

• Although there is no class named Tomo, I believe that createTomo shows the meanings of "creating an object representing tomo-seq data" better than checkTomo, so I leave this name unchanged.

• More details in documentation are added.

• GetMatrix is replaced with assay. Accessing matrices using assay is demonstrated in the vignette.

• cat and print is replaced with message.

• hierarchClust (old name HClust) returns a hclust object so it cannot be added into createTomo. Besides, I plan to add more clustering algorithms in future versions, so I do not think adding clustering functions in createTomo is a good idea.

• Functions using data of certain assays now have the augument matrix, which tells the functions which assay to work on. Default values are provided so that users do not always need to specify it.

• assays are replaced with assay.

• Allocate and fill strategy is used in FindPeakGene.

README.md

There is BiocManager::install("tomoda") in Installation.

[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: "WARNINGS". 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/tomoda 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: 1233335b2ebcd93acccefeda53f3304184fad8ce

[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/tomoda to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[LiNk-NY]

Hi Wendao Liu, @liuwd15

Thank you for making those changes. They look great! I would consider renaming the createTomo.matrix function into something that resembles an S3 method less. Perhaps tomoMatrix? I will accept your package. Thank you for your contribution.

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!

[liuwd15]

Hi Marcel @LiNk-NY, Thanks for reviewing and accepting this package. createTomo.matrix and createTomo.SummarizedExperiment are renamed into tomoMatrix and tomoSummarizedExperiment now.

Best, Wendao

[LiNk-NY]

Great!

[mtmorgan]

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