search

cytoscape / RCy3

New version of RCy3, redesigned and collaboratively maintained by Cytoscape developer community
MIT License
50 stars 20 forks source link

The images are not appearing in the Cancer Network and Data vignette #102

Closed jeffreyblanchard closed 3 years ago

jeffreyblanchard commented 3 years ago

Thanks for putting this package together. Just a note to let you know that the images are not appearing in the Cancer Network and Data vignette. Take Care, Jeff

AlexanderPico commented 3 years ago

The Rmd is produced as an html here: https://cytoscape.org/cytoscape-automation/for-scripters/R/notebooks/Cancer-networks-and-data.nb.html

Can you point to where they are not showing up? Perhaps you mean while you are running the Rmd yourself? I don't think it was designed to work that way. If you have suggested edits to add them, please submit a PR. Thanks!

jeffreyblanchard commented 3 years ago

Hi Alexander,

What you just sent looks fine.  When in R

browsevignettes("RCy3)

If I click on the html.

Take Care, Jeff

On 11/16/20 1:29 PM, Alexander Pico wrote:

The Rmd is produced as an html here: https://cytoscape.org/cytoscape-automation/for-scripters/R/notebooks/Cancer-networks-and-data.nb.html https://cytoscape.org/cytoscape-automation/for-scripters/R/notebooks/Cancer-networks-and-data.nb.html

Can you point to where they are not showing up? Perhaps you mean while you are running the Rmd yourself? I don't think it was designed to work that way. If you have suggested edits to add them, please submit a PR. Thanks!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/cytoscape/RCy3/issues/102#issuecomment-728244263, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABCM35TAB6CWOZHVRRDBFFLSQFVSLANCNFSM4TXDHDKA.

AlexanderPico commented 3 years ago

Ah, got it. I see it now. Looking into a fix...

Bioconductor has their own build system. I only provide the Rmd and the rest comes from them... and they don't have Cytoscape installed in their build rigs :)

HOWEVER, looking deeper, it seems like I can provide images along with my Rmd files. I'll give that a try in the next release!