convert KEGGgraph.Rnw to KEGGgraph.Rmd #16
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vignettes/KEGGgraph.Rmd
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| well as a collection of tools to analyze, dissect and visualize these graphs. | ||
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| The package requires KGML (KEGG XML) files, which can be downloaded from KEGG | ||
| REST web service ((https://rest.kegg.jp/)) without license permission for |
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This should have one set of parenthesis.
vignettes/KEGGgraph.Rmd
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| * Manual download from KEGG REST API, documented at at (https://www.kegg.jp/kegg/rest/keggapi.html). | ||
| * Automatic retrieval from KEGG REST API, available at (https://rest.kegg.jp), |
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Remove the parentheses from URLs in lines 91 and 92.
vignettes/KEGGgraph.Rmd
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| ``` | ||
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| Pathways and their identifiers can be browsed in the KEGG website | ||
| (https://genome.jp/kegg), or found with any search engine. |
vignettes/KEGGgraph.Rmd
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| The subgraph is visualized in figure [1](#fig:01), where nodes with in-degree or | ||
| out-degree in red and others in grey [^1]. And in the example we also | ||
| demonstrate how to convert KEGG ID into other other identifiers via the Entrez | ||
| GeneID. More details on the conversion of IDs can be found on section [Annotation](#convertId) |
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Let's improve the wording a little with in the [Annotation section](#convertId). and add a full stop at the end.
vignettes/KEGGgraph.Rmd
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| To convert GeneID to other identifiers, we recommend genome wide annotation | ||
| packages, for human it is `r Biocpkg("org.Hs.eg.db")` and the packages for other | ||
| organisms can be fount at | ||
| (http://www.bioconductor.org/packages/release/data/annotation/). To demonstrate |
vignettes/KEGGgraph.Rmd
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| packages, for human it is `r Biocpkg("org.Hs.eg.db")` and the packages for other | ||
| organisms can be fount at | ||
| (http://www.bioconductor.org/packages/release/data/annotation/). To demonstrate | ||
| its use, we draw the sub-network in the figure [2](fig:02) again, whereas nodes |
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The link doesn't work; maybe it's missing the #?
| *Note*: the current version of `RBGL` (version 1.59.5) reports the error that | ||
| `BGL_brandes_betweeness_centrality` not available for `.Call()` for package | ||
| `r Biocpkg("RBGL")`. Therefore the execution has been suppressed for now. |
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@Accio I just wanted to make a note of this section that references RBGL 1.59.5 (it's now 1.79.0).
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@sonali8434 Thanks for this PR. I've made some small inline requests. The DESCRIPTION file should have VignetteBuilder: knitr and BiocStyle, knitr in Suggests. Because this is missing, R CMD build isn't generating the vignette.
I also want to confirm with @Accio if the new bibliography format is suitable as it presents the reference differently. For example
Current:
[Aittokallio and Schwikowski, 2006] Aittokallio and Schwikowski (2006) Graph-based methods for analysing networks in cell biology, Briefings in Bioinformatics, 7, 243-255.
Newer:
Aittokallio and Schwikowski (2006) Graph-based methods for analysing networks in cell biology. Briefings in Bioinformatics, 7, 243–255.
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@jwokaty Thanks for the review, and I'm sorry for not pushing my changes to the description file. Thanks for reminding me. I have made the changes you asked for. Please review. |
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@sonali8434 Thanks for the changes. This is ready for @Accio.
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Dear @sonali8434 and @jwokaty, I agree with the changes you proposed. Thank you for making them. Do you mind adding yourself as contributors in the DESCRIPTION file? I am glad to merge the changes once the testing passes. Have a good day and thanks again for the generous help, David. |
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@Accio, I have completed the remaining changes. Please review the file and let me know if any more changes are required. Thank you. |
@jwokaty kindly Review this PR before we ask @Accio for a final review.
@Accio We noticed that this pdf contains sections referring to pages, but it is not possible to refer to pages in new .Rmd file since we don't have a page no in an HTML document. So we have referred to sections instead of pages in the new KEGGgraph.Rmd file. If you have any suggestions about this, please don't hesitate to let us know.
We generally ask one of our team members to review the conversions before asking the maintainers to review them.
@Accio Generally, we give credits to the converter for converting Sweave documents. We ask maintainers if they want us to add ourselves as contributors in the description file and the. Rmd file. I wanted to ask if you would like me to add as a contributor for this conversion. It's totally fine to say no.
After your final review when you merge the PR, remember to bump the version in the DESCRIPTION file so that the Bioconductor build system will recognize the new changes and push the changes to Bioconductor's git repository.