cbioportal/oncoprintjs

OncoPrint visualization

[DEPRECATED] In favor of monorepo, oncoprintjs library has been moved under cBioPortal/cbioportal-frontend. This repo is no longer maintained.

oncoprintjs's Issues

WebserviceParserUtils exception

org.mskcc.cbio.portal.web_api.ProtocolException
at org.mskcc.cbio.portal.util.WebserviceParserUtils.getSampleIds(WebserviceParserUtils.java:77)
at org.mskcc.cbio.portal.servlet.WebService.getClinicalData(WebService.java:416)
at org.mskcc.cbio.portal.servlet.WebService.processClient(WebService.java:232)
at org.mskcc.cbio.portal.servlet.WebService.doPost(WebService.java:125)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:647)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:728)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.mskcc.cbio.portal.util.XssFilter.doFilter(XssFilter.java:65)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:186)
at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:160)
at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:344)
at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:261)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.apache.catalina.filters.CorsFilter.handleNonCORS(CorsFilter.java:439)
at org.apache.catalina.filters.CorsFilter.doFilter(CorsFilter.java:178)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:99)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:953)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
at org.apache.coyote.ajp.AjpProcessor.process(AjpProcessor.java:200)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:589)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:310)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)

Track labels overlap tracks on firefox

Track labels are on top of the tracks in firefox instead of side by side in chrome.

Define input format for npm package

Make npm package that produces SVG files

TODO:

• Define input format
• Unit tests
• Publish to npm

testing

Plan
(1) Set up standard oncoprint set up, as a playground for tests.
(2) Go through recent pull requests and write tests for them.

Installation errors

Hi I am having trouble installing oncoprintjs on my macbook pro. I have tried installing oncoprintjs on my Mac and in a docker running unbuntu and keep getting the same error. I don't think it is an oncoprintjs error per se, but a problem with the installation. Any guidance is appreciated.

gulp spec
[09:16:58] Using gulpfile ~/oncoprintjs/gulpfile.js
[09:16:58] Starting 'spec'...
[09:16:58] 'spec' errored after 31 ms
[09:16:58] Error in plugin 'gulp-jasmine'
Message:
Cannot find module '../../src/js/sorting.js'
Details:
code: MODULE_NOT_FOUND

Sorting algorithm

Hi,

I tried to understand how the samples where sorted using http://www.cbioportal.org/oncoprinter.jsp with the default example data but I failed. At first, I thought that was given the natural order of the genes to sort the tracks on Y, and then the samples (on X) were sorted given the natural order of the samples of the first gene. This obviously is not correct.

I found out that we could maybe sort the events alphabetically but this, again, was not correct. I tried to dig into the source code of this lib but I got lost and I don't really find good resources on this. Is there a de facto sorting algorithm for OncoPrint charts? I have read about mutual exclusivity, like here where the "memo sort" is mentioned but this paper talks about something slightly different if I am not mistaken. Given that there has different versions of the OncoPrint, I am not sure where to find the information, hence this issue.

I hope someone could help me figure out how to sort the genes, samples and events as done on the cBioPortal. Thank you for your help.

License change to AGPL?

The code of cBioPortal is licensed as AGPL. This is licensed as ISC. Should we change the license or do we prefer the more permissive license for oncoprint? I'm just opening this issue because I've heard different things from @n1zea144 and @jjgao. Including @adamabeshouse @gideonite in the discussion.

Blank page when running test page

Hi. I followed the README and when I went to localhost:8000, it just showed a blank page. It returned a HTTP 200 response, so there doesn't seem to be any issues on that end. Is there something else I'm suppose to do? Like add something to the index.html?

support sortBy function

This would allow a radix sort, which could greatly speed up genetic track sorting

Naming

I think we may be having a naming issue - there are several things that just don't seem to have a natural name, and so we are ad-hoc making names for them in the code. I think it would be best if, at this point, we standardized terms for various elements of the oncoprint.

My main thrust here is to decouple visual concepts from biological concepts.
The most obvious motivator for this is the mild confusion that arises when we have to deal with whether columns represent samples or patients, but we still refer to/think about each cell as a 'sample'. It would be better, I think, to just call them 'cells' and couple the concepts elsewhere in the code.

As far as generality, if we want to add to the oncoprint later, it will be easier to make sense of what's going on if we don't have to reckon with using a visualization that's named after one biological concept to also refer to a similar yet technically distinct biological concept.

In short, this will make it easier to add to the oncoprint in the future, and will make it easier for us to mentally organize the code.

I've attached a Google slide and my proposals (based on what's in the code, and some ideas of my own). Go ahead and make changes/suggestions in the slides and let's figure it out together!

Some things you might do:

• challenge/endorse a name thats in there, or suggest a different name
• raise something that needs to be named that's not represented in the slide
• argue this isn't necessary 😛

https://docs.google.com/presentation/d/1Q9m2SZfW2XIbX4PIi2d4BtbBD1En_nJHChWoOlw2fkE/edit?usp=sharing

show nice message if webGL context fails, dont throw exception to console

README.md python -m SimpleHTTPServer doesn't work

When following the instructions in the readme serving the page using Python's SimpleHTTPServer doesn't work:

cd dist/test && python -m SimpleHTTPServer

The JS error is:

test-oncoprint-bundle.js:1323 Uncaught SyntaxError: Unexpected token ILLEGAL
localhost/:31 Uncaught ReferenceError: testscript is not defined

No problems using http-server though.

missing 'gl-matrix' as dependency in package.json

'gl-matrix' package required by oncoprintwebglcellview.js is not listed as dependency in package.json.
Due to this, npm install would result in the following error: Error: Cannot find module 'gl-matrix'

Development setup fails to build

When I follow the instructions on how to build the playground, gulp fails with the following error message:

[12:47:48] Using gulpfile ~/git/oncoprintjs/gulpfile.js
[12:47:48] Starting 'default'...
Error: Cannot find module 'worker-loader?inline=true&fallback=false!./workers/clustering-worker.js' from '/Users/fedde/git/oncoprintjs/src/js'
    at /Users/fedde/git/oncoprintjs/node_modules/browser-resolve/node_modules/resolve/lib/async.js:46:17
    at process (/Users/fedde/git/oncoprintjs/node_modules/browser-resolve/node_modules/resolve/lib/async.js:173:43)
    at ondir (/Users/fedde/git/oncoprintjs/node_modules/browser-resolve/node_modules/resolve/lib/async.js:188:17)
    at load (/Users/fedde/git/oncoprintjs/node_modules/browser-resolve/node_modules/resolve/lib/async.js:69:43)
    at onex (/Users/fedde/git/oncoprintjs/node_modules/browser-resolve/node_modules/resolve/lib/async.js:92:31)
    at /Users/fedde/git/oncoprintjs/node_modules/browser-resolve/node_modules/resolve/lib/async.js:22:47
    at FSReqWrap.oncomplete (fs.js:152:21)
[12:47:49] 'default' errored after 963 ms
[12:47:49] Error in plugin "gulp-shell"
Message:
    Command `browserify src/js/main.js -o dist/oncoprint-bundle.js` failed with exit code 1

NullPointerException in CrossCancerStudyServlet related to XssFilter

java.lang.NullPointerException
at org.mskcc.cbio.portal.servlet.CrossCancerStudyServlet.doPost(CrossCancerStudyServlet.java:94)
at org.mskcc.cbio.portal.servlet.CrossCancerStudyServlet.doGet(CrossCancerStudyServlet.java:81)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:621)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:728)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.mskcc.cbio.portal.util.XssFilter.doFilter(XssFilter.java:65)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:186)
at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:160)
at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:344)
at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:261)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.apache.catalina.filters.CorsFilter.handleNonCORS(CorsFilter.java:439)
at org.apache.catalina.filters.CorsFilter.doFilter(CorsFilter.java:178)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:99)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:953)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
at org.apache.coyote.ajp.AjpProcessor.process(AjpProcessor.java:200)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:589)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:310)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)

iam not able to generate rules param

i am using plain java script to generate visualisation, iam not able to understand how to generate rule_params it is giving error, can anybody help me how to generate rules_param
i need to generate 4-5 different rows

1. stacked bar
2. bar
3. count

Write unit tests