Convert matchprobes.Rnw to matchprobes.Rmd

Bioconductor / Biostrings

Efficient manipulation of biological strings

https://bioconductor.org/packages/Biostrings

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Convert matchprobes.Rnw to matchprobes.Rmd #86

Closed hsadia538 closed 1 year ago

hsadia538 commented 1 year ago

Part of Sweave2rmd project.

Creates a vignette in R markdown which replaces the sweave vignette.
Attached are the HTML vignette and Sweave for comparison here

matchprobes.Rnw matchprobes.Rmd

hsadia538 commented 1 year ago

@jwokaty Please take a look. Thanks

mcarlsn commented 1 year ago

@jwokaty I will take a first pass reviewing this PR.

jwokaty commented 1 year ago

@hsadia538 I made a few changes to the code, which you can see at https://github.com/Bioconductor/Biostrings/pull/86/commits/32998032059ac47768053b96d846b2958949a72c. Thanks for working on this.

@hpages Could I ask you to review and accept if it is okay? I made a small change on lines 118-126 (see below) so that the value could be displayed on the HTML. Maybe there's another way to do this with just nc = hgu95av2dim$NCOL that I just didn't know.

nc = hgu95av2dim$NCOL
nc

nr = hgu95av2dim$NROW
nr

Thanks for your time.

hsadia538 commented 1 year ago

Hi @jwokaty I see this PR is still open. Do you want me to close it?

jwokaty commented 1 year ago

Hi @jwokaty I see this PR is still open. Do you want me to close it?

@hsadia538 Let's keep it open for now as @hpages should review but I know he's quite busy. We'll close it if is needed.

hpages commented 1 year ago

oops, missed this. Let me take a look. I'll get back to you before the end of the week.

hpages commented 1 year ago

I think you want to use eval=FALSE here, instead of message=FALSE (opening the man page with ?hgu95av2probe only makes sense in interactive mode, not when knitting the vignette):
```
  ```{r hgu95av2probe,message=FALSE}
  ?hgu95av2probe
```
Space is missing in figure caption "... to the number of probeswith ..."
Last figure (Figure 3) does not show up for me in the HTML vignette after rendering it with rmarkdown::render("matchprobes.Rmd"). Looks like this in the old PDF vignette: You want to make sure that no figure gets lost in the translation from Rnw to Rmd.
Also, probably related to the above, I get "See Figures 1-??" in the HTML vignette:

Screenshot from 2023-02-23 17-04-18

Thanks!

hpages commented 1 year ago

@hsadia538 @mcarlsn @jwokaty Is someone going to follow up on this PR?

jwokaty commented 1 year ago

@hpages I made the changes since they were small.