Converting IntroToAnnotationDbi.Rnw to Rmarkdown #9

BerylKanali · 2023-02-14T15:17:38Z

@jwokaty
Here is a draft pull request.
The issue is, I need help to figure out what library or a way I can use to automatically section the exercise and solution bit (line 186- 280) like it was done in the Rnw file using the Theorem package:

%% Question, Exercise, Solution
\usepackage{theorem}
\theoremstyle{break}
\newtheorem{Ext}{Exercise}
\newtheorem{Question}{Question}

\newenvironment{Exercise}{
  \renewcommand{\labelenumi}{\alph{enumi}.}\begin{Ext}%
}{\end{Ext}}
\newenvironment{Solution}{%
  \noindent\textbf{Solution:}\renewcommand{\labelenumi}{\alph{enumi}.}%
}{\bigskip}

If not, I can do it manually.
PDF file
HTML file so far

Note: Replaced the dataTypes pdf image file to png for better output.

jwokaty · 2023-02-17T22:02:58Z

AFAIK there's no automatic way to convert these and I don't think there is an equivalent in R Markdown. It is possible to mock this up in HTML just using R Markdown to make it look similar to the PDF manually then remove the section, like the one above, since it would no longer be used.

LiNk-NY · 2023-02-17T22:26:48Z

You can create a <details> html tag in the vignette to hide or show the solution, e.g.,

<details> Solution <summary> Here is the solution </summary>
## R code chunk of the solution
</details>

There is also the learnr package for shiny documents but the infrastructure is more involved and it requires a shiny dependency.

BerylKanali · 2023-03-02T12:30:39Z

@jwokaty
Added some commits here and switched it from draft to ready for review.
Updated HTML

sonali8434 · 2023-06-19T08:42:43Z

DESCRIPTION

vignettes/IntroToAnnotationPackages.Rmd

sonali8434

Hello @BerylKanali Thanks for your PR, during the review process I noticed that there are many instances where we need a space between two words please correct the instances like these and let me know I will continue the review process.

BerylKanali · 2023-07-06T14:14:53Z

Hi @sonali8434 I made the changes, here is the updated HTML file.

sonali8434

Hello @BerylKanali Thank you for the changes I have completed the review Please do these modifications after that this PR will be ready for the final review.

I noticed that you have not italicized the objects in many instances please correct that rest everything looks good.

vignettes/IntroToAnnotationPackages.Rmd

Merge branch 'AnnotationDbi-Rmd' of https://github.com/BerylKanali/AnnotationDbi into AnnotationDbi-Rmd # Please enter a commit message to explain why this merge is necessary, # especially if it merges an updated upstream into a topic branch. # # Lines starting with '#' will be ignored, and an empty message aborts # the commit.

BerylKanali · 2023-07-20T14:43:38Z

@sonali8434 Thank you for your review, I have made the changes. Here is the updated HTML file.

sonali8434 · 2023-07-20T20:13:21Z

Hello, @BerylKanali Thank you so much for the quick edits; just two small changes then it will be ready for @jwokaty.

sonali8434 · 2023-07-20T20:16:19Z

Hello @jwokaty, The review of this file is complete. You can do a final review after these two changes are addressed.
I have checked R CMD build and HTML in the tarball

Thank you!!

jwokaty

@BerylKanali There are a few more changes. Mostly changes to remove Biocpkg() from things aren't packages. The easiest way to always check is to click on the link of the generated html. There were also 2 package names in the original that weren't correct, preventing the link from being generated properly. We'll be able to merge after these corrections.

The exercise-solution sections look good. Thanks for your work on this!

jwokaty · 2023-07-21T17:14:53Z

vignettes/IntroToAnnotationPackages.Rmd

+
+- Organism level: e.g. `r Biocpkg("org.Mm.eg.db")`. 
+- Platform level: e.g. `r Biocpkg("hgu133plus2.db")`, 
+`r Biocpkg("hgu133plus2.probes")`, `r Biocpkg("hgu133plus2.cdf")` 


Maybe these were renamed or misspelled in the original document? Biocpkg can't make links for these, but I did find packages hgu133plus2probe and hgu133plus2cdf. Could you update line 37 with these?

jwokaty · 2023-07-21T17:17:31Z

vignettes/IntroToAnnotationPackages.Rmd

+
+# ChipDb objects and the select method
+
+An extremely common kind of `r Biocpkg("Annotation")` package is the so called


I think the writer is speaking generally about Annotation packages but not a specific package named Annotation. Remove

`r Biockpg("")`

jwokaty · 2023-07-21T17:19:19Z

vignettes/IntroToAnnotationPackages.Rmd

+(e.g. Entrez Gene id) and contains mappings between this identifier and other
+kinds of identifiers (e.g. GenBank or Uniprot accession number, RefSeq id,
+etc.). The name of an org package is always of the form org.\<Ab>\.\<id>\.db
+(e.g.`r Biocpkg("org.Sc.sgd.db")`where \<Ab>\ is a 2-letter abbreviation of the


Add a closing parenthesis and space between the last backtick and where so that we have

(e.g.`r Biocpkg("org.Sc.sgd.db")`) where

jwokaty · 2023-07-21T17:19:59Z

vignettes/IntroToAnnotationPackages.Rmd

+`r Biocpkg("sgd")` for gene identifiers assigned by the Saccharomyces Genome
+Database, or `r Biocpkg("eg")` for Entrez Gene ids).


sgd and eg are not packages. Remove

`r Biocpkg("")`

jwokaty · 2023-07-21T17:20:57Z

vignettes/IntroToAnnotationPackages.Rmd

+kinds of identifiers (e.g. GenBank or Uniprot accession number, RefSeq id,
+etc.). The name of an org package is always of the form org.\<Ab>\.\<id>\.db
+(e.g.`r Biocpkg("org.Sc.sgd.db")`where \<Ab>\ is a 2-letter abbreviation of the
+organism (e.g.`r Biocpkg("Sc")` for *Saccharomyces cerevisiae*) and \<id>\ is an


Sc is not a package. Remove

`r Biocpkg("")`

jwokaty · 2023-07-21T17:25:20Z

vignettes/IntroToAnnotationPackages.Rmd

+
+# Using select with TxDb packages
+
+A `r Biocpkg("TxDb")` package (a 'TxDb' package) connects a set of genomic


TxDb is not a package, but a type of package. Remove

`r Biocpkg("")`

jwokaty · 2023-07-21T17:40:46Z

vignettes/IntroToAnnotationPackages.Rmd

+  - name: "Marc Carlson"
+  - name: "Beryl Kanali"
+    affiliation: "Converted vignette from Sweave to Rmarkdown"
+date: "Last modified: November 2022; Compiled: `r format(Sys.time(), '%B %d , %Y')`"


Remove Last modified: November 2022; Compiled: . I don't know where the November 2022 date comes from.

jwokaty · 2023-07-21T18:12:22Z

vignettes/IntroToAnnotationPackages.Rmd

+
+# Using select with GO.db
+
+When you load the ` r Biocpkg("GO.db")` package, a *GODb* object is also loaded.


Remove the space after the first backtick (otherwise it doesn't render the link properly).

Convert file to Rmd

20a7e7f

BerylKanali and others added 2 commits February 23, 2023 04:08

Update Rmd file

3c659a7

Update DESCRIPTION

1132c5c

BerylKanali marked this pull request as ready for review March 2, 2023 12:01

BerylKanali added 3 commits March 2, 2023 07:07

update Rmd contents

29bbca9

delete Rnw file

5d66af6

marge branch with remote

2fc3d08

sonali8434 reviewed Jun 19, 2023

View reviewed changes

sonali8434 suggested changes Jun 19, 2023

View reviewed changes

BerylKanali and others added 2 commits July 6, 2023 08:32

Update Rmd file

161d09f

Update DESCRIPTION

6c696dd

sonali8434 suggested changes Jul 18, 2023

View reviewed changes

BerylKanali and others added 3 commits July 20, 2023 09:28

Update Rmd after review

dd17213

Merge branch 'devel' into AnnotationDbi-Rmd

9437cdc

jwokaty requested changes Jul 21, 2023

View reviewed changes

jwokaty assigned BerylKanali Jul 21, 2023


		# ChipDb objects and the select method

		An extremely common kind of `r Biocpkg("Annotation")` package is the so called

		`r Biocpkg("sgd")` for gene identifiers assigned by the Saccharomyces Genome
		Database, or `r Biocpkg("eg")` for Entrez Gene ids).


		# Using select with TxDb packages

		A `r Biocpkg("TxDb")` package (a 'TxDb' package) connects a set of genomic


		# Using select with GO.db

		When you load the ` r Biocpkg("GO.db")` package, a GODb object is also loaded.

Converting IntroToAnnotationDbi.Rnw to Rmarkdown #9

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sonali8434 commented Jun 19, 2023 •

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