Use of png images

[drisso]

Hi,

in last year's workshop, we started our Rmd file with a schema of a typical single-cell workflow, which we included simply by using

knitr::include_graphics("schema_workflow.png")

That means including a (small) png file to the repository. Is that OK, or is it discouraged?

[risserlin]

I have the same question. Would it be ok to add a directory called images and put all my images in it?

[mtmorgan]

Without knowing the technical details, I think there should be structure so each workshop is acting +/- independently of the other, e.g., a folder rather than top-level Rmd file for each workshop. That way one can at least associate images & other resources with workshops, and one knows who to contact if things get out of hand...

[sa-lee]

I'm also interested in this - @mtmorgan is what you're suggesting to go for something like:

./Lee_Plyranges/
    Lee_Plyranges.Rmd
    ref.bib
    figures/

and set the fig.path option in the Rmd file?

[mtmorgan]

@sa-lee yep exactly

[LiNk-NY]

I don't think this current structure is supported for bookdown. See here: rstudio/bookdown#107
It seems like all Rmd files should be in the root folder and data / image files etc. could be in a folder.

Alternative:

./Lee_Plyranges.Rmd
./Lee_Plyranges
    ref.bib
    figures/

[LiNk-NY]

Note: PNGs are preferred especially when building the PDF version of the book.