dphansti / coral Goto Github PK

I realize the posting are years old, but I am hoping for some help anyway. The R directory in the coral.tar download appears to have useful tools. However I have not succeeded with implementing them in R. In particular the convertID.R script may be helpful in dealing with various labels. I have successfully sourced global.R and loaded all libraries, however where to go from here is not clear. Any chance there is a more detailed readme or help file?

Thanks

From @dphansti:

... While I think the app is good enough, I really wish the D3 plots had legends. If you load example data and look at the 'Tree' plot you'll see that legends are automatically generated...

Can we remove the radialNetworkR package from the loaded package set? It isn't available for R 3.4.3 and it doesn't appear to be still in development. I'm not familiar enough with the workings of the network portion of the code to know if I can safely be removed.

From @dphansti:

The D3 plots (circle and force) are a bit buggy. The force network tends to freak out when you make too many changes to the settings. This may just be how it is. I am not sure if there is a clear 'fix' for it.

I think the repo is missing a set of png's that are supposed to be in the www/images folder.

When i am running the app following error occuring :

shiny::runApp()
Loading required package: shiny
Attaching package: ‘shinydashboard’
The following object is masked from ‘package:graphics’:
box
Attaching package: ‘colourpicker’
The following object is masked from ‘package:shiny’:
runExample
Attaching package: ‘DT’
The following objects are masked from ‘package:shiny’:
dataTableOutput, renderDataTable
Attaching package: ‘jsonlite’
The following object is masked from ‘package:shiny’:
validate
Listening on http://127.0.0.1:7122
Warning: Error in get: object 'controlLabel' not found
93: get
92: :::
89: radioButtons_withHTML [R/radiobuttonswithimages.R#19]

hello.
I want to utilize Kinome map for Coral. I want to modify the tree, but I was wondering if you could share how to create the tree. Now, by understanding the code, it seems to be svg creation through tsv -> tree.rds file creation -> rendering through rds file.

I've been using the IDs from HGNC:

https://www.genenames.org/

Any chance those could be added to the valid name list?

Did you move a few files out of www and into a folder named "tempfiles". I was trying to sync up your latest commits, but the tempfiles folder doesn't seem to be syncing from your repository.

Hi, the graphs of Coral look nice and I would like to draw some kinome trees with it. I tried to use your web application http://phanstiel-lab.med.unc.edu/CORAL/. I first specify the "node color" with categorical input of 25 kinases. Before the graph is updated, the error shows up "disconnected from the server". How can I fix this? Thank you!

I have been unable to get CORAL to work in a windows or linux application, and am seeking guidance. I have downloaded the CORAL-master utilities
(ui.R, global.R, server.R, Coral.proj, README.md and the directories www, R and Data). Following the steps in global.R, the correct libraries have been loaded into R (3.3.2). Since I am attempting to implement in the R package on a windows and linux machine, the ‘data.tree’ package presented most of the problems. When the appropriate packages were installed, the library(‘data.tree’) finally worked for both machines.

install.packages("data.tree" , dependencies=T) did not pick up the needed packages, so each was done separately. Regardless, all the libraries could be loaded and the sourced *.R files yielded no errors.
However, in both the windows and linux machines

source(‘global.R’) gives the same error

rna_data = paste(readLines("Data/RNAdata.txt"),collapse="\n")
Warning message:
In readLines("Data/RNAdata.txt") :
incomplete final line found on 'Data/RNAdata.txt'

rna_abs_data = paste(readLines("Data/RNAdata_pluripotent.txt"),collapse="\n")
Warning message:
In readLines("Data/RNAdata_pluripotent.txt") :
incomplete final line found on 'Data/RNAdata_pluripotent.txt'

I inspected both files and added a \n to the final line, without success.

Any suggestions would be most appreciated.

I would also ask about the D3.js java script library. I have not encountered a java ‘hook’ in R. I have downloaded D3.js to the CORAL-master directory.
Is there a pointer for that location that needs to be run within R?

Finally, I am looking forward to generating images using CORAL. Your ‘examples’ are quite impressive, however, a suite of sample scripts would be helpful (or a pdf writeup). If this information is available at http://phanstiel-lab.med.unc.edu/CORAL/ please direct me to where. So far I do not seem to have the capacity to implement anything. I would add the >source(‘./R/Test.R’), does not generate any of the output expected from this script.

Thanks in advance for your help,

David Covell, Ph.D.
NIH-NCI

From @dphansti:

"Force/Circle graphs were not "contained" within the window" (this is actually browser specific. The problem definitely occurs on chrome but not Safari I think).

From the reviewers:

2. The Circle and Force Graph modes are difficult to work with. [The comment above applies here, too.]

During testing, it often happened that the whole graph would tumble off screen and couldn't be re-centered without returning to Tree and then back to Force or Circle. If it didn't leave the screen entirely, it would move in a way that made it hard to focus on the nodes of interest. Unlike the Tree view, Force/Circle graphs were not "contained" within the window, which again made them difficult to work with. It wasn't entirely clear to us what the Force Graph would be used for, since they are typically used to visualize network data, though perhaps other users would have a need.

Example overflow (when both graphs are zoomed in):