Statial

[fame2827]

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• Repository: https://github.com/SydneyBioX/Statial

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[bioc-issue-bot]

Hi @fame2827

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: Statial
Type: Package
Title: A package to identify changes in cell state relative to spatial associations
Version: 0.99.0
Date: 2022-09-19
Authors@R: c(person("Farhan", "Ameen", email = "fame2827@uni.sydney.edu.au",
    role = c("aut", "cre")),
    person("Sourish", "Iyengar", email = "sourish.iyengar@sydney.edu.au",
    role = c("aut")),
    person("Shila", "Ghazanfar", email = "shila.ghazanfar@sydney.edu.au",
    role = c("aut")),
    person("Ellis", "Patrick", email = "ellis.patrick@sydney.edu.au",
    role = c("aut")))
VignetteBuilder: knitr
Encoding: UTF-8
biocViews: SingleCell, Spatial
Depends: R (>= 4.1.0)
Imports: 
    BiocParallel,
    spatstat.geom,
    concaveman, 
    tidyverse,
    data.table, 
    spatstat.core,
    dplyr, 
    spatstat, 
    tidyr, 
    SingleCellExperiment,
    tibble,
    stringr,
    tidyselect,
    ggplot2,
    methods,
    stats
Suggests: BiocStyle, knitr
Description: Statial is a suite of functions for identifying changes in cell 
    state. The functionality provided by Statial provides robust quantification 
    of cell type localisation which are invariant to changes in tissue 
    structure. In addition to this Statial uncovers changes in marker expression
    associated with varying levels of localisation. These features can be used 
    to explore how the structure and function of different cell types may be 
    altered by the agents they are surrounded with.
License: GPL-3
RoxygenNote: 7.2.1

[vjcitn]

Your README.md has "The goal of betAS is to ... This is a line from RStudio".

[fame2827]

Hi @vjcitn looks like you might have the wrong package :)

[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/Statial 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: e4a80139576d2e31c81c3deb78fafbd623ff9ceb

[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/Statial 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: 592938864793d8d3f69691c90c1aeaa2688b887c

[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/Statial 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: 686ef975a00cbbc9415215ace8752581a5ea3af8

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

[DarioS]

Statial is a package for analysing colocalisation of cell types. Its relevance to Bioconductor is strong. My findings are: • The vignette has a good introduction to the problem domain and it introduces a timely and relevant data set for demonstrating the functionality of the package. • Please update installation instructions to use BiocManager instead of devtools. • The cellType vector is confusing. It is more of a cell ID rather than a cell type. It looks like you manually type out the cell types instead (e.g. bcells <- c("BC1", "BC2", "BC3")). If the user has one thousand cells, do they have to type out each one of the one thousand cells, like the example code shows? • Scatter plot. Make the plot area smaller and the axes font size bigger to improve readability. • Vignette mentions Keren et al. 2018 and Ferguson et al. 2022. Please provide full references at the end of the vigette. • A recent requirement of Bioconductor packages is Unit Tests. Most of your functions need to have unit tests. See the developer's guide for more guidance about those. • The documentation of exported functions is brief. You need a Description section and, sometimes, also a Details section. • Use vapply instead of for loops where applicable. See also Vectorize section.

parentDfs <- list()
for (i in seq_along(names(parentList))) {
  parentDfs[[i]] <- crossing(
  from = parentList[[i]],
  parent_name = names(parentList)[i])
}

Your code has for loop structures which could easily be converted into the Bioconductor requirement. • Please use informative variable names that would be easily understood by a new programmer reading the code.

p$d <- cut(p$d, Rs, labels = Rs[-1], include.lowest = TRUE)
w <- rep(1, length(X))
p$wt <- rep(1, length(p$d))

All these single-character variable names are hard to read and not consistent with the principle of self-documenting code. • Only one function, inhomL, depends on data.table. Could you achieve the same result in another way and avoid this package dependency to make package installation and loading slightly faster? • Some robustness against incorrect user input would be beneficial. For example, if cells is not either a SingleCellExperiment or list or SpatialExperiment, then it won't be caught and notified to the end user. • SpatialExperiment is just mentioned once in the repository.

cells: A SingleCellExperiment or SpatialExperiment or a list of single images.

Does the package provide interoperability with SpatialExperiment or not? Given that it is a spatial omics data analysis package, I think users would naively expect it to have interoperability with SpatialExperiment. Also, for "a list of single images", what class does each element of the list need to have? Explicitly state this somewhere.

[fame2827]

Hi Dario, thanks for your feedback! Regarding the cellType vector, these are in fact cellTypes the Ferguson data unfortunately has cellType names which look like cellIDs. I do agree it's confusing, would you have any suggestions on how I can make this clearer?

[DarioS]

Ah, now I get it! They are basically different subtypes of a cell type. This data could be ideal for TreeSummarizedExperiment.

TreeSummarizedExperiment has extended SingleCellExperiment to include hierarchical information on rows or columns.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 2b49daa60fc583471de511fb0dacb9d7aac9eb10

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

[fame2827]

@DarioS I have addressed most of the feedback. Regarding the data.table import, data.table speeds up the inhomL function considerably which, if not included would slow down every function in Statial. At the cost of slightly slower import times, could I leave this import in, so that the overall package performs efficiently.

In the meantime I will be updating the descriptions sections of documentation. Let me know what you think!

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: ac640116531a6279e22b0b1db61cd6093b033bee

[DarioS]

That's a good plan. Think of Title ≡ one sentence and Description ≡ one paragraph.

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

[bioc-issue-bot]

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

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[lshep]

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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

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

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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.