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poem
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- Repository: https://github.com/RoseYuan/poem
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Hi @RoseYuan
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: poem
Title: POpulation-based Evaluation Metrics
Version: 0.99.1
Authors@R: c(
person("Siyuan", "Luo", email="[email protected]", role=c("cre","aut"), comment=c(ORCID="0009-0007-6404-3244")),
person("Pierre-Luc", "Germain", email="[email protected]", role=c("aut","ctb"),
comment=c(ORCID="0000-0003-3418-4218")))
Description: Implements a set of (mostly external) evaluation metrics for comparing partitions,
fuzzy partitions, for evaluating the segregation of classes/clusters in embeddings or graphs, etc.
Also includes metrics for comparing spatial data to ground truth labels and spatially visualizing
errors.
BugReports: https://github.com/RoseYuan/poem/issues
License: GPL (>= 3)
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Depends:
R (>= 4.0)
Imports:
aricode,
BiocNeighbors,
BiocParallel,
bluster,
clevr,
clue,
cluster,
elsa,
fclust,
igraph,
Matrix,
mclustcomp,
methods,
sp,
spdep,
stats,
utils
Suggests:
testthat (>= 3.0.0),
BiocStyle,
knitr,
DT,
dplyr,
scico,
cowplot,
ggnetwork,
ggplot2,
tidyr
VignetteBuilder: knitr
biocViews: DimensionReduction, Clustering, GraphAndNetwork, Spatial
Config/testthat/edition: 3
Bioconductor would like a clean repository on our system. Please remove pkgdown and Dockerfiles from default branch until after it has been cloned onto out system.
Is there a way to include a Bioconductor specific example in the vignette to show how this would work practically into a workflow and show interoperability with a common Bioconductor object/analysis? Perhaps with a SpatialExperiment object
Hi @lshep , I'm just curious about your comment that "Bioconductor would like a clean repository on our system." Does that mean you want it clean only for the submission? I (like a lot of people I suppose) keep github and Bioc in sync for all my packages to facilitate maintenance, so that even if it was "clean" upon submission it's not anymore after it's been included. Is this considered an issue or not? Thanks in advance, Pierre-Luc
Meaning the version we have on git.bioconductor.org should not contain developmental extras. After submission you could still keep a separate branch that removes those items and restore a default branch (ie. a branch called devel that is in sync with bioconductor and everything on a main branch less those features)
Hi @lshep,
We now have a clean devel branch as required, and we added a new vignette for our package titled "Working with SpatialExperiment" to show the interoperability with Bioconductor. Please let us know if you have further comments. Thanks.
Best regards,
Siyuan
Your package has been added to git.bioconductor.org to continue the pre-review process. A build report will be posted shortly. Please fix any ERROR and WARNING in the build report before a reviewer is assigned or provide a justification on why you feel the ERROR or WARNING should be granted an exception.
IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. All changes should be pushed to git.bioconductor.org moving forward. It is required to push a version bump to git.bioconductor.org to trigger a new build report.
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Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
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.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 24.04.1 LTS): poem_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
[email protected]:packages/poem to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 39b4332db7e6ebcbb53b7ebd584489dd6b1a3966
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
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.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 24.04.1 LTS): poem_0.99.3.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
[email protected]:packages/poem to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 692f5a30a4a8c4229b66fe0ed7f3a1521f98e564
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
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 Single Package Builder: Linux (Ubuntu 24.04.1 LTS): poem_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
[email protected]:packages/poem to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.
I apologize for the delay, I was away on holiday. I should have a review today or tomorrow at the latest.
Thank you for your patience. Here is the following review. Please let us know when we should re-review the package by doing a version bump and triggering a new build and by commenting addressing the following:
README
- [ ] Update with Bioconductor installation
data-raw/man data
- [ ] Can you move these to an
inst/scripts/directory where we generally recommend having scripts that generate data. Likely you should reference these scripts in the man pages for the data. The man pages for the data are currently very minimal and should include any relevant source/licensing information or say it is simulated.
docs
- [ ] Please remove docs directory from Bioconductor repository.
tests
- [ ] It would be nice to improve testing coverage
> library(covr)
> package_coverage()
poem Coverage: 41.70%
R/getFuzzyPartitionMetrics.R: 0.00%
R/getGraphElementMetrics.R: 0.00%
R/getSpatialExternalMetrics.R: 0.00%
R/getSpatialInternalMetrics.R: 0.00%
R/spatial.R: 0.00%
R/SpatialMetrics.R: 0.00%
R/fuzzyPartitionMetrics.R: 21.30%
R/getPartitionMetrics.R: 32.14%
R/utils.R: 43.81%
R/metrics.R: 47.54%
R/getGraphClassMetrics.R: 65.88%
R/getPartitionGlobalMetrics.R: 81.25%
R/getGraphMetrics.R: 83.33%
R/simulation.R: 83.87%
R/CDbw.R: 85.29%
R/dbcv.R: 86.73%
R/getEmbeddingMetrics.R: 95.52%
R/getPartitionClassMetrics.R: 95.96%
vignette
poem
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[ ] Update with Bioconductor installation
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[ ] Please mention the other vignettes that deal with Bioconductor objects in the introduction.
SpatialExperiment
- [ ] Please change the name to avoid conflicts as this will conflict with the SpatialExpeirment vignette directly.
> vignette("SpatialExperiment")
Warning message:
vignette 'SpatialExperiment' found more than once,
using the one found in '/home/lorikern/R-Libraries/R4.5-Bioc3.21/poem/doc'
- [ ] You hid the library calls of your vignette so if a user directly tries to run the code there is an error
spe <- Visium_humanDLPFC()
Error in Visium_humanDLPFC() :
could not find function "Visium_humanDLPFC"
- [ ] Your functions should work directly with SpatialExperiment Objects rather than extracting data frames. You should be able to store results as additional entries to the SpatialExperiment Object.
table
-
[ ] Seems an odd name for a vignette?
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[ ] Could you add an introduction to explain what these are and how they are relevant in the package?
R code
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[ ] Please fix R CMD check and BiocCheck warnings/notes.
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[x] Please check values of arguments to ensure user is giving proper type/values.
We thank you for your interest and look forward to working to getting your package into Bioconductor. Cheers
Hi @lshep , thank you for your reviews. We've been working on resolving them, and regarding your comments
Can you move these to an inst/scripts/ directory where we generally recommend having scripts that generate data. Likely you should reference these scripts in the man pages for the data.
I'm wondering what would be the best way to refer to scripts in the man pages. Should I refer to an url of the script on github? Or the directory of the script in that package (like inst/scripts/noisy_moon.R)?
Best, Siyuan
Hi @lshep,
For your comments about the vignette poem:
Please mention the other vignettes that deal with Bioconductor objects in the introduction.
Could you specify what that means?
Thanks and best, Siyuan
You can do something like
dataScript <- system.file('scripts', 'sp_toys.R', package='poem')
Your main vignette and what people will likely find first is the vignette named "poem" , vignette("poem") ... but that vignette doesn't show interactions with Bioconductor objects; this is in a separate vignette you provide (SpatialExperiment.Rmd -- we still would like this renamed so it doesn't clash with the actual SpatialExperiment vignette) . So please make reference to the other vignette in the poem vignette that can redirect Bioconductor users to the appropriate vignette
You can do something like
dataScript <- system.file('scripts', 'sp_toys.R', package='poem')
You mean it's possible to run the code you wrote here in line of documentation?
I wouldn't run it. I would mention in the documentation for the data -- that the scripts to generate the data can be viewed at dataScript <- system.file('scripts', 'sp_toys.R', package='poem') this will give the location of for instance the sp_toys.R script but not run it
By moving data generation scripts to inst/scripts/ you actually mean poem/scripts in this case, right?
Dear @lshep ,
We discussed together regarding this point:
Your functions should work directly with SpatialExperiment Objects rather than extracting data frames. You should be able to store results as additional entries to the SpatialExperiment Object.
We can write a method so that the wrapper for spatial metrics can be given a SpatialExperiment as input, however we're not comfortable having it output a populated SpatialExperiment. While this would work well for element-wise metrics, it would feel a bit random for metrics computed at other levels (i.e. where to store them isn't clear, and the variable naming would get complicated if the user wants to compute metrics for multiple methods). So if that's okay with you we'd implement something that takes a SE as input, but lets the user put back the results in it where applicable, e.g. something like:
res_element <- getSpatialExternalMetrics(SE, clusters=SE$clusters, level="element")
colData(SE) <- cbind(colData(SE), res_element)
Does that sound like a reasonable compromise to you?
Thanks for all the feedback,
Pierre-Luc
Received a valid push on git.bioconductor.org; starting a build for commit id: f4dbf35905607473b668040df3a32ebd3c1c4101
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
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.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 24.04.1 LTS): poem_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
[email protected]:packages/poem to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 6724bd056d098cd1ee85f397c25895ff2005f786
Dear Package contributor,
This is the automated single package builder at bioconductor.org.
Your package has been built on the Bioconductor Single Package Builder.
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.
The following are build products from R CMD build on the Single Package Builder: Linux (Ubuntu 24.04.1 LTS): poem_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
[email protected]:packages/poem to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.
Received a valid push on git.bioconductor.org; starting a build for commit id: 7e621fccf0d5def99c342c7d6bd399c625dcc4f8