setEdgeLineWidthBypass errors

[m-grimes]

Alex I've been using code you sent to me previously to set edge line widths according to values in the data as shown below. Something is not working that I don't understand. Thanks, Mark

edgevalues <- getTableColumns('edge',c('name','Weight')) edgevalues['Weight']<-abs(edgevalues['Weight']) edgevalues['Weight']<-lapply(edgevalues['Weight'], function(x) x * 5) setEdgeLineWidthBypass(edgevalues[['name']], edgevalues[['Weight']])

Errors:

RCy3::cyrestPUT, HTTP Error Code: 500 url=http://localhost:1234/v1/networks/60252/views/90343/edges?bypass=TRUE body=[ { "SUID": 65537, "view": [ { "visualProperty": "EDGE_WIDTH", "value": 0.003550924 } ] }, { "SUID": 65536, "view": [ { "visualProperty": "EDGE_WIDTH", "value": 1.38 } ] }, { "SUID": 65539, "view": [ { "visualProperty": "EDGE_WIDTH", "value": 0.002013419 } ] }, ...

Goes on and on

sessionInfo() R version 3.5.2 (2018-12-20) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS High Sierra 10.13.6 RCy3_2.2.6

[AlexanderPico]

Here's a toy example that works. Careful running this, however, as it will open a new session and close your current one (unsaved).

openSession()
edgevalues <- getTableColumns('edge',c('name','EdgeBetweenness'))
edgevalues['EdgeBetweenness']<-abs(edgevalues['EdgeBetweenness'])
edgevalues['EdgeBetweenness']<-lapply(edgevalues['EdgeBetweenness'], function(x) x / 2000)
setEdgeLineWidthBypass(edgevalues[['name']], edgevalues[['EdgeBetweenness']])

If this works for you, then we can suspect something particular about your network. Can you share it or a sample from it?

[m-grimes]

Thanks Alex. But

Error in commandsPOST(paste0("session open ", type, "=\"", 

file.location, : File 'Yeast Perturbation.cys' not found:

Mark

---

Mark Grimes Division of Biological Sciences University of Montana Missoula, Montana 59812-4824 Grimes lab website Office Telephone: (406) 243-4977 Fax Number: (406) 243-4184 E-mail: Mark.Grimes@mso.umt.edu

On 25 Feb 2019, at 16:20, Alexander Pico wrote:

Here's a toy example that works. Careful running this, however, as it will open a new session and close your current one (unsaved).

openSession()
edgevalues <- getTableColumns('edge',c('name','EdgeBetweenness'))
edgevalues['EdgeBetweenness']<-abs(edgevalues['EdgeBetweenness'])
edgevalues['EdgeBetweenness']<-lapply(edgevalues['EdgeBetweenness'], 
function(x) x / 2000)
setEdgeLineWidthBypass(edgevalues[['name']], 
edgevalues[['EdgeBetweenness']])

If this works for you, then we can suspect something particular about your network. Can you share it or a sample from it?

-- You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub: https://github.com/cytoscape/RCy3/issues/45#issuecomment-467224858

[AlexanderPico]

Here's how I would do it:

edgevalues <- getTableColumns('edge',c('Weight'))
edgevalues['Weight']<-abs(edgevalues['Weight'])
edgevalues['Weight']<-lapply(edgevalues['Weight'], function(x) x * 5)
names(edgevalues)<-c('Width')
loadTableData(edgevalues, table = 'edge', table.key.column = 'SUID')
setEdgeLineWidthMapping('Width', mapping.type = 'passthrough', style.name = 'Crizotinib PTM Style')

Try to avoid using Bypasses whenever possible. They are slow; they are not saved with a style; they stick to a particular network view. I only recommend them for a handful of things that you really must override. But you can almost always simply create a new column and make a mapping instead.

[m-grimes]

Thanks Alex. This is a new function that appears to replace setEdgeLineWidthRule(net.w, edge.attribute.name="Weight", attribute.values=net.edges$Weight, line.widths=net.edges$Weight)

Your code did not give the same error, but did not change the edge witdths, just turned all the edges white (which I'd set as default previously). See screenshot.

• mark

[m-grimes]

Note that I got your code to work with a small network, just not the large one. Not sure why. I'll try plotting the large network from scratch again.

[m-grimes]

I going to close this for now until I can figure out the issue with the big network.

• Mark