Update documentation #81

noriakis · 2023-08-30T03:18:18Z

Hello, I have updated the documentation of tidySummarizedExperiment to be consistent with tidyseurat and tidySingleCellExperiment. Currently, R CMD CHECK runs without errors, warnings, or notes.

utilities.R has not been touched for formatting unless it needs to be changed to avoid errors, as it has already been edited.
se object initialization has been added to unite, separate, extract to avoid R CMD CHECK NOTEs.

I would be grateful if you could review the changes.

- comments in slice example are preserved

data.R ggplot2_methods.R methods.R plotly_methods.R print_method.R

cleaning R CMD CHECK

stemangiola · 2023-09-07T07:01:44Z

R/utilities.R

-                nest(data___ = c(!!s_(se)$symbol, !!f_(se)$symbol, value)) %>%
+                nest(data___ = c(!!s_(se)$symbol, !!f_(se)$symbol, .data$value)) %>%


the tidy evaluation works without the .data$ Any specific reason you add all those?

Thank you for the review. The inclusion of .data$ was intended to address the NOTEs raised by R CMD CHECK regarding undefined global variables. If necessary, I can revert these changes.

stemangiola · 2023-09-07T07:14:17Z

@noriakis please have a look to the github actions

noriakis · 2023-09-07T10:43:19Z

Thank you for the review. For GiHub actions, I am currently looking for a way to resolve WARNINGs. On R 4.3.1, the rcmdcheck runs without problems. However, on R 4.2.2, the same warnings as for GitHub actions appear in my environment.

4.2.2

── R CMD check results ────────────────────────────────────────────────────────────────── tidySummarizedExperiment 1.11.4 ────
Duration: 4m 33.5s

❯ checking whether package 'tidySummarizedExperiment' can be installed ... WARNING
  See below...

❯ checking S3 generic/method consistency ... WARNING
  Warning: declared S3 method 'count.SummarizedExperiment' not found
  Warning: declared S3 method 'filter.SummarizedExperiment' not found
  Warning: declared S3 method 'rename.SummarizedExperiment' not found
  Warning: declared S3 method 'slice.SummarizedExperiment' not found
  See section 'Generic functions and methods' in the 'Writing R
  Extensions' manual.

0 errors ✔ | 2 warnings ✖ | 0 notes ✔

4.3.1

── R CMD check results ──────────────────── tidySummarizedExperiment 1.11.4 ────
Duration: 5m 10.7s

0 errors ✔ | 0 warnings ✔ | 0 notes ✔

stemangiola · 2023-09-07T12:42:15Z

@HelenaLC maybe knows how to solve this mystery

stemangiola · 2023-09-14T01:45:26Z

NAMESPACE

+export(bind_cols.RangedSummarizedExperiment)
+export(bind_cols.SummarizedExperiment)
+export(bind_rows.SummarizedExperiment)


Please have a look, if these are present in tidySingleCellExperiment as well, because they look a bit strange

I believe it should look like

https://github.com/stemangiola/tidySingleCellExperiment/blob/a3dc67e2c72b6eacd954b202d9fcb61fc246b0b1/NAMESPACE#L6

Hello, thank you very much for the prompt reply. I apologize for the commit without the comment.

The warnings above (count, filter, rename, slice) were solved by moving dplyr to Depends (https://stat.ethz.ch/pipermail/r-devel/2014-June/069247.html), however, in that way, the other warnings that methods lookup cannot find bind_cols and bind_rows occurred as below. The additional @export was the intention to avoid these warnings.

W checking S3 generic/method consistency (5.7s) Warning: declared S3 method 'bind_cols.RangedSummarizedExperiment' not found Warning: declared S3 method 'bind_cols.SummarizedExperiment' not found Warning: declared S3 method 'bind_rows.SummarizedExperiment' not found See section 'Generic functions and methods' in the 'Writing R Extensions' manual.

tidyseurat also has these warnings when checked in R 4.2.3, and tidySingleCellExperiment also has them as below if I explicitly change R version dependency and check in R 4.2.3, although these warnings will not occur as tidySingleCellExperiment depends on R >= 4.3.0.

W checking S3 generic/method consistency (7.5s) Warning: declared S3 method 'bind_cols.SingleCellExperiment' not found Warning: declared S3 method 'bind_rows.SingleCellExperiment' not found See section 'Generic functions and methods' in the 'Writing R Extensions' manual.

I would say, let's depend on anything tidySCE depends on, and let's set up the github action from tidySCE template.

Basically whatever tidySCE does we do as well.

I apologize that no checks have been made on BiocCheck in this PR. Will remove at least errors.

You can check the package locally and then push it. We are getting close!

Thanks! Just added a runnable example in plotly.Rd. The commit locally passed BiocCheck (in 3.18) without errors (warnings and notes remained, also in tidySCE). R CMD CHECK (version 4.3.1) also passes without errors, warnings, and notes, which should pass GitHub actions.

changed R dependency to >= 4.3.0

stemangiola · 2023-09-14T08:56:13Z

Congrats! Well done, and thanks! If you feel to contribute more there are so many possibilities.

noriakis · 2023-09-18T03:02:44Z

Thank you very much for approving the PR and for your guidance! Will update the tidyseurat workflow shortly to be in line with tidySCE.

stemangiola · 2023-09-18T03:09:34Z

Thank you very much for approving the PR and for your guidance! Will update the tidyseurat workflow shortly to be in line with tidySCE.

If I'm not wrong, tidyseurat documentation has been fixed already. What do you mean by workflow?

I tagged you in a Documentation tidybulk issue, to provide guidance.

noriakis · 2023-09-18T09:14:44Z

Sorry for the delay in response and for the unclear description. I meant to say the update of GitHub Actions workflow to be compatible with tidySCE one as I did in tidySE, which includes the checks in the R version 4.3 and the latest BiocCheck (3.18). If needed, I will proceed.

Also, thank you for mentioning in tidybulk, I will check and update the answer shortly.

stemangiola · 2023-09-18T09:21:42Z

Yes

noriakis and others added 5 commits August 27, 2023 16:42

update dplyr methods

5e9bb5f

- comments in slice example are preserved

update documentations

defd391

data.R ggplot2_methods.R methods.R plotly_methods.R print_method.R

update remaining documentations

b39d804

cleaning R CMD CHECK

fixed wrong return values

cd1dba6

Merge branch 'master' into update-documentation

65c8bfd

stemangiola reviewed Sep 7, 2023

View reviewed changes

Remove warnings of rcmdcheck in R 4.2

45d7ef3

stemangiola reviewed Sep 14, 2023

View reviewed changes

noriakis added 2 commits September 14, 2023 12:58

revert the changes and update workflow

9a5c96e

changed R dependency to >= 4.3.0

Solve Bioc error

0270570

stemangiola merged commit dcfb940 into stemangiola:master Sep 14, 2023
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stemangiola linked an issue Sep 16, 2023 that may be closed by this pull request

Improve the documentation of tidytranscriptomics adapters, tidySE, tidySCE, tidySPE, tidyseurat stemangiola/tidyseurat#66

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stemangiola mentioned this pull request Sep 18, 2023

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Update documentation #81

Update documentation #81

noriakis commented Aug 30, 2023

stemangiola Sep 7, 2023

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stemangiola commented Sep 7, 2023

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noriakis commented Sep 18, 2023

stemangiola commented Sep 18, 2023

noriakis commented Sep 18, 2023

stemangiola commented Sep 18, 2023

		nest(data___ = c(!!s_(se)$symbol, !!f_(se)$symbol, value)) %>%
		nest(data___ = c(!!s_(se)$symbol, !!f_(se)$symbol, .data$value)) %>%

Update documentation #81

Update documentation #81

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stemangiola commented Sep 14, 2023

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