Error in buildNode

[jpropa25]

Hello,

I've been trying to run the GScluster function and had been running up against an error. Finally, I tried just running the sample code and got the same error, so I'm wondering what I can do to troubleshoot:

`data=GetGSASNP2Data(filename='https://github.com/unistbig/GScluster/raw/master/inst/GScluster/GSASNP2_DIAGRAM.txt')
GSAresult = data$GSAresult
GeneScores = data$GeneScores
GScluster(GSAresult = GSAresult, GeneScores = GeneScores, Species = 'H', alpha = 1, GsQCutoff = 0.25, GQCutoff = 0.05)
[1] "PPI table is not given, STRING data is used."

Listening on http://127.0.0.1:7313
Warning: Error in buildNode: id must be string
53: stop
52: buildNode
51: RenderGeneSetNetwork [/usr/local/lib/R/3.6/site-library/GScluster/GScluster/app.R#1262]
50: server [/usr/local/lib/R/3.6/site-library/GScluster/GScluster/app.R#1289]
Error in buildNode(id = nodes[i, 1], bgColor = nodes[i, 3], labelColor = "black", :
id must be string`

Any input would be really appreciated.

Thanks,
Jim

[jhk0530]

Hi,

thanks for notice me error.
I found what was problem. and it fixed. 👍
also you can check reason for GScluster not worked ( it's my mistake, sorry )
these code will work after re-install GScluster using this code

remotes::install_github('unistbig/GScluster')
library(GScluster)

If this works on you well or have any problems, please let me know.

Regards.
Kim

# code you mentioned

data=GetGSASNP2Data(filename='https://github.com/unistbig/GScluster/raw/master/inst/GScluster/GSASNP2_DIAGRAM.txt')
GSAresult = data$GSAresult
GeneScores = data$GeneScores
GScluster(GSAresult = GSAresult, GeneScores = GeneScores, Species = 'H', alpha = 1, GsQCutoff = 0.25, GQCutoff = 0.05)

library(GScluster)
GScluster()

what was problem?

in GSCluster, we use shinyCyJS package to visualize graph with cytoscape.js.

and recently we're working on that package to submit to CRAN which requires quite strict conditions.

while that process, I restricted each graph's node should accept only character or string term in buildNode function.

And we found that GScluster didn't follow that rule, it gives factor data to shinyCyJS.

Which is really really unintended behavior.

so I fixed GScluster to give characater data.

[jpropa25]

It is getting me to the network page now, which is a great improvement from what I was seeing- thanks! However, now I am getting the following error message (I also get a message in the web browser NO genes with cutoff when I try clicking on "Show PPI"):

Listening on http://127.0.0.1:6813
Warning in observeEventHandler(...) : NAs introduced by coercion
Warning: Error in [: subscript out of bounds
110: which
109: FUN [/usr/local/lib/R/3.6/site-library/GScluster/GScluster/app.R#378]
108: lapply
107: sapply
105: GetHubGenes [/usr/local/lib/R/3.6/site-library/GScluster/GScluster/app.R#377]
104: BuildMultiHub [/usr/local/lib/R/3.6/site-library/GScluster/GScluster/app.R#543]
103: exprFunc
102: widgetFunc
101: func
88: origRenderFunc
87: renderFunc
83: origRenderFunc
82: output$tab2
2: shiny::runApp
1: GScluster

Thanks for developing a really cool tool. I think it's a really awesome tool in theory- I'm hoping to debug some of this so that I will get good use out of it in practice.

Best,
Jim

[jhk0530]

Could you give me the situation you've tried? like

• after run ~~ data
• ~~ button with ~option.

It'll be really helpful to investigate problems.

Usually, No genes with cutoff will shown,

when user used too high value in PPI Cutoff slider, and GScluster didn't get any result with that cutoff. so using lower value may solve that problem.

Also, if you want to debug this, you can fork repository to your own repository and

open GScluster.Rproj with Rstudio.

Thanks.