230_Isserlin_RCy3_intro.Rmd

[lwaldron]

I'm creating an issue for each workshop, to be closed when both 1) the workshop is complete, and 2) it compiles without problems. Please note problems and status updates here.

ERROR: cytoscapeVersionInfo not found

[risserlin]

in order for the function to work Cytosacpe needs to be opened. Should I put all of cytoscape commands in if blocks? (If I do that the notebook won't have any of the figures that are generated when the notebook can talk to cytoscape.

[lwaldron]

What I suggest is to put eval=FALSE for this code block, but insert a screenshot of the figure in your workshop. That way students can run Cytoscape interactively, but we can still build the book showing what they should see.

[risserlin]

I have added screenshots for all the cytoscape commands and disabled them with an eval. I still want to add one last use case and polish it but hopefully it should compile now.

[lwaldron]

Make sure to pull or merge these changes before further editing. I am getting an error:

Quitting from lines 1001-1016 (230_Isserlin_RCy3_intro.Rmd) 
Error in data.frame(name = ora.all$res.tbl$GENE.SET, descr = ora.all$res.tbl$GENE.SET,  : 
  arguments imply differing number of rows: 9002, 0
Calls: <Anonymous> ... withCallingHandlers -> withVisible -> eval -> eval -> data.frame
Execution halted

[risserlin]

I fixed the above error.

[LiNk-NY]

Hi Ruth, @risserlin Thanks for fixing that. I updated your workshop front matter by removing it. Bookdown Rmd files work slightly differently than a regular Rmd.

[risserlin]

I just realized that my references are not associated with my individual notebook but instead are at the end (in chapter 16). The document was supposed to finalized yesterday. Is it ok to check in my notebook again minus the "References" heading I have at the end of my notebook?