escheR #2988

boyiguo1 · 2023-03-28T20:13:47Z

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bioc-issue-bot · 2023-03-28T20:13:49Z

Hi @boyiguo1

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: escheR
Title: Unified multi-dimensional visualizations with Gestalt principles
Version: 0.99.0
Authors@R: c(
    person("Boyi", "Guo",
 email = "boyi.guo.work@gmail.com", role = c("aut", "cre"),
 comment = c(ORCID = "0000-0003-2950-2349")),
    person(c("Stephanie", "C."), "Hicks",  role = c("aut"), 
  email = "shicks19@jhu.edu", 
  comment = c(ORCID = "0000-0002-7858-0231"))
  )
Description: The creation of effective visualizations is a fundamental component
    of data analysis. In biomedical research, new challenges are emerging to 
    visualize multi-dimensional data in a 2D space, but current data 
    visualization tools have limited capabilities. To address this problem,
    we leverage Gestalt principles to improve the design and interpretability
    of multi-dimensional data in 2D data visualizations, layering aesthetics
    to display multiple variables. The proposed visualization can be applied
    to spatially-resolved transcriptomics data, but also broadly to data
    visualized in 2D space, such as embedding visualizations. We provide this
    open source R package escheR, which is built off of the state-of-the-art
    ggplot2 visualization framework and can be seamlessly integrated into
    genomics toolboxes and workflows.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
biocViews: 
    Spatial, 
    SingleCell,
    Transcriptomics,
    Visualization,
    Software
Depends:
    ggplot2   
Imports: 
    SpatialExperiment (>= 1.6.1),
    spatialLIBD,
    rlang,
    SummarizedExperiment
BugReports: https://github.com/boyiguo1/escheR/issues
URL: https://github.com/boyiguo1/escheR
Suggests: 
    STexampleData, 
    knitr,
    rmarkdown
VignetteBuilder: knitr

bioc-issue-bot · 2023-04-03T13:10:12Z

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bioc-issue-bot · 2023-04-03T13:26:45Z

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: "skipped, TIMEOUT".
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
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A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot · 2023-04-03T14:26:34Z

Received a valid push on git.bioconductor.org; starting a build for commit id: d282c3f3aa4c55015dd24576e9e643f135a43228

bioc-issue-bot · 2023-04-03T14:35:08Z

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.
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Please see the build report for more details. This link will be active
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Remember: if you submitted your package after July 7th, 2020,
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bioc-issue-bot · 2023-04-03T18:16:01Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 6b1432abeba54e8e522710658f02ad84bf058da7

bioc-issue-bot · 2023-04-03T18:24:38Z

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
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A quick tutorial for setting up remotes and pushing to upstream can be found here.

jianhong · 2023-04-05T12:51:58Z

Package 'escheR' Review

Thank you for submition your package to Bioconductor. The package passed check and build. It is in pretty good shape. However there are several things need to be fixed. Please try to answer the comments line by line when you are ready for a second review.
Code: Note: please condsider; Important: must be addressed.

The DESCRIPTION file

R version is not clear in DESCRIPTION.

The NAMESPACE file

Selective imports using importFrom instead of import all with import.
- in line 8 import(SpatialExperiment)
- in line 9 import(ggplot2)
- in line 10 import(spatialLIBD)

R code

Important: No paste in message(), message, stop
- In file R/add_fill.R:
  - at line 34 found ' stop(paste0("Please add the variable ", var, " to colData(spe)."))'
- In file R/add_ground.R:
  - at line 37 found ' stop(paste0("Please add the variable ", var, " to colData(spe)."))'
- In file R/add_symbol.R:
  - at line 36 found ' stop(paste0("Please add the variable ", var, " to colData(spe)."))'
NOTE: :: is not suggested in source code unless you can make sure all the packages are imported. Some people think it is better to keep ::. However please note that you need to manully double check the import items when you make any change in the DESCRIPTION file during development. My recommendation is to remove one or two repeats to force the dependency check.
- In file R/make_escheR.R:
  - at line 58 found ' d <- as.data.frame(cbind(colData(spe), SpatialExperiment::spatialCoords(spe)), optional = TRUE)'
  - at line 64 found ' SpatialExperiment::imgRaster('
  - at line 86 found ' x = pxl_col_in_fullres * SpatialExperiment::scaleFactors(spe, sample_id = sampleid, image_id = image_id) - adjust$x,'
  - at line 87 found ' y = pxl_row_in_fullres * SpatialExperiment::scaleFactors(spe, sample_id = sampleid, image_id = image_id) - adjust$y,'
Important: 1:n is not suggested in source code. Use seq_along or seq.int instead.
- In file R/add_fill.R:
  - at line 59 found ' # setNames(c(paste0("L", 1:6), "WM", "NA", "WM2"))'
Important: Remove unused code.
- In file R/add_fill.R:
  - at line 31 found ' # browser()'
  - at line 37 found ' # if(is.numeric(p$data[,var])) {'
  - at line 38 found ' # stop("")'
  - at line 39 found ' # p <- suppressMessages({p + scale_fill_continuous()})'
  - at line 40 found ' # } else{'
  - at line 41 found ' # p <- suppressMessages({p + scale_fill_discrete()})'
  - at line 42 found ' # }'
  - at line 45 found ' # browser()'
  - at line 54 found ' # if(!is.numeric(p$data[,var]))'
  - at line 55 found ' # tmp <- tmp +'
  - at line 56 found ' # scale_fill_manual('
  - at line 57 found ' # name = "",'
  - at line 58 found ' # values = libd_layer_colors |>'
  - at line 59 found ' # setNames(c(paste0("L", 1:6), "WM", "NA", "WM2"))'
  - at line 60 found ' # )'
  - at line 63 found ' # tmp$scales <- tmp$scales[[-1]]'
- In file R/make_escheR.R:
  - at line 51 found ' ## (http://spatial.libd.org/spatialLIBD/)'
NOTE: Avoid 'suppressWarnings'/'*Messages' if possible
- In file R/add_fill.R:
  - at line 39 found ' # p <- suppressMessages({p + scale_fill_continuous()})'
  - at line 41 found ' # p <- suppressMessages({p + scale_fill_discrete()})'
NOTE: Functional programming: code repetition.
- repetition in add_fill and add_ground and add_symbol
  - in add_fill
    - line 1: point_size = 2, ...)
    - line 2:{
    - line 3: if (!is.character(var) || length(var) != 1) {
    - line 4: stop("The argument var must be character of length one.")
    - line 5: }
    - line 6: if (!var %in% colnames(p$data)) {
    - line 7: stop(paste0("Please add the variable ", var, " to colData(spe)."))
    - line 8: }
    - line 9: p + geom_point(aes(fill = !!sym(var)), shape = 21, stroke = 0,
  - in add_ground
    - line 1: var, stroke = 0.5, point_size = 2, ...)
    - line 2:{
    - line 3: if (!is.character(var) || length(var) != 1) {
    - line 4: stop("The argument var must be character of length one.")
    - line 5: }
    - line 6: if (!var %in% colnames(p$data)) {
    - line 7: stop(paste0("Please add the variable ", var, " to colData(spe)."))
    - line 8: }
    - line 9: p + geom_point(aes(color = !!sym(var), ), shape = 21, fill = "transparent",
  - in add_symbol
    - line 1: var, size = 1, ...)
    - line 2:{
    - line 3: if (!is.character(var) || length(var) != 1) {
    - line 4: stop("The argument var must be character of length one.")
    - line 5: }
    - line 6: if (!var %in% colnames(p$data)) {
    - line 7: stop(paste0("Please add the variable ", var, " to colData(spe)."))
    - line 8: }
Note: move theme in function make_escheR.SpatialExperiment to a sub_function.
Note: Use dots to pass parameters to geom_point in add_symbol function and add_fill function and let user to overwrite the defaults.

Documentation

Important: Please include Bioconductor installation instructions using BiocManager.
- rmd file vignettes/SRT_eg.Rmd
Note: Vignette includes motivation for submitting to Bioconductor as part of the abstract/intro of the main vignette.
- rmd file vignettes/SRT_eg.Rmd

bioc-issue-bot · 2023-04-05T17:57:00Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 434f5faae140f57fb2456e67054dc0bbe9190038

bioc-issue-bot · 2023-04-05T18:05:28Z

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

boyiguo1 · 2023-04-05T18:16:52Z

Dear @jianhong,

Thank you very much for your careful review. I have addressed all the important comments and most of the notes. The rest of the unaddressed notes will be considered in the next update of escheR.

Please find the line-by-line response to your comments at boyiguo1/escheR#4.

My responses are highlighted in

Response: italic font.

Please find all changes to the escheR package in the recent pull request at boyiguo1/escheR#6.

Again, thank you very much for your review. Please let me know if there is anything else I need to address for this submission.

Sincerely,
Boyi

jianhong · 2023-04-05T18:56:02Z

Great Job. Just update your R dependence version from current >=3.6 to >=4.3.0 will be OK for acception. This is required by Bioconductor.

Jianhong.

bioc-issue-bot · 2023-04-05T19:55:21Z

Received a valid push on git.bioconductor.org; starting a build for commit id: 5982d360b0a69c055c7f67d534fed5802bbe0547

bioc-issue-bot · 2023-04-05T20:05:04Z

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

bioc-issue-bot · 2023-04-05T20:09:06Z

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.

boyiguo1 · 2023-04-05T20:10:08Z

@jianhong Thank you very much for your feedback!

lshep · 2023-04-10T14:57:46Z

The default branch of your GitHub repository has been added to Bioconductor's
git repository as branch devel.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/boyiguo1.keys is not empty), then no further steps are required. Otherwise, do the following:

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/
https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

(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("escheR"). The package 'landing page' will be created at

https://bioconductor.org/packages/escheR

If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.

bioc-issue-bot added the 1. awaiting moderation submitted and waiting clearance to access resources label Mar 28, 2023

vjcitn added the pre-check passed pre-review performed and ready to be added to git label Apr 1, 2023

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boyiguo1 mentioned this issue Apr 5, 2023

Bioconductor Submission Review boyiguo1/escheR#4

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escheR #2988

escheR #2988

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escheR #2988

escheR #2988

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jianhong commented Apr 5, 2023

Package 'escheR' Review

The DESCRIPTION file

The NAMESPACE file

R code

Documentation

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