{"action":"created","comment":{"url":"https://api.github.com/repos/cBioPortal/cbioportal-frontend/pulls/comments/276938170","pull_request_review_id":228632612,"id":276938170,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDI3NjkzODE3MA==","diff_hunk":"@@ -130,24 +129,42 @@ export interface IScatterPlotSampleData {\n     profiledMutations?:boolean;\n     mutations: AnnotatedMutation[];\n     copyNumberAlterations: AnnotatedNumericGeneMolecularData[];\n+    xThresholdType?: '>'|'<'|undefined; // threshold symbol for x coordinate in scatter plot\n+    yThresholdType?: '>'|'<'|undefined; // threshold symbol for y coordinate in scatter plot\n+    thresholdType?: '>'|'<'|undefined; // threshold symbol for continuous axis in box-scatter and waterfall plot\n }\n \n-export interface IScatterPlotData extends IScatterPlotSampleData, IBaseScatterPlotData {};\n-\n-export interface IBoxScatterPlotPoint extends IScatterPlotSampleData {\n+export interface IBoxScatterPlotPoint extends IPlotSampleData {\n     category:string;\n     value:number;\n     jitter:number;\n }\n \n+export interface IWaterfallPlotSampleData extends IPlotSampleData {\n+    sortOrder:string;\n+    pivotThreshold:number;\n+}\n+\n+export interface IScatterPlotData extends IPlotSampleData, IBaseScatterPlotData {};\n+export interface IWaterfallPlotData extends IWaterfallPlotSampleData, IBaseWaterfallPlotData {};\n+\n+export interface IAxisLogScaleParams {\n+    label:string;\n+    fLogScale:((x:number, offset:number)=>number);","path":"src/pages/resultsView/plots/PlotsTabUtils.tsx","position":149,"original_position":149,"commit_id":"d873c174a4ad84425d34b83d14655bd155d4facc","original_commit_id":"a679c9e42294ef683784c2468885ad1af4998859","user":{"login":"pvannierop","id":745885,"node_id":"MDQ6VXNlcjc0NTg4NQ==","avatar_url":"https://avatars0.githubusercontent.com/u/745885?v=4","gravatar_id":"","url":"https://api.github.com/users/pvannierop","html_url":"https://github.com/pvannierop","followers_url":"https://api.github.com/users/pvannierop/followers","following_url":"https://api.github.com/users/pvannierop/following{/other_user}","gists_url":"https://api.github.com/users/pvannierop/gists{/gist_id}","starred_url":"https://api.github.com/users/pvannierop/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pvannierop/subscriptions","organizations_url":"https://api.github.com/users/pvannierop/orgs","repos_url":"https://api.github.com/users/pvannierop/repos","events_url":"https://api.github.com/users/pvannierop/events{/privacy}","received_events_url":"https://api.github.com/users/pvannierop/received_events","type":"User","site_admin":false},"body":"Comment added.","created_at":"2019-04-19T08:54:17Z","updated_at":"2019-04-19T08:54:17Z","html_url":"https://github.com/cBioPortal/cbioportal-frontend/pull/2055#discussion_r276938170","pull_request_url":"https://api.github.com/repos/cBioPortal/cbioportal-frontend/pulls/2055","author_association":"CONTRIBUTOR","_links":{"self":{"href":"https://api.github.com/repos/cBioPortal/cbioportal-frontend/pulls/comments/276938170"},"html":{"href":"https://github.com/cBioPortal/cbioportal-frontend/pull/2055#discussion_r276938170"},"pull_request":{"href":"https://api.github.com/repos/cBioPortal/cbioportal-frontend/pulls/2055"}},"in_reply_to_id":275949616},"pull_request":{"url":"https://api.github.com/repos/cBioPortal/cbioportal-frontend/pulls/2055","id":254666611,"node_id":"MDExOlB1bGxSZXF1ZXN0MjU0NjY2NjEx","html_url":"https://github.com/cBioPortal/cbioportal-frontend/pull/2055","diff_url":"https://github.com/cBioPortal/cbioportal-frontend/pull/2055.diff","patch_url":"https://github.com/cBioPortal/cbioportal-frontend/pull/2055.patch","issue_url":"https://api.github.com/repos/cBioPortal/cbioportal-frontend/issues/2055","number":2055,"state":"open","locked":false,"title":"Integration of treatment response data in PlotsTab (incl. new Waterfall plot)","user":{"login":"pvannierop","id":745885,"node_id":"MDQ6VXNlcjc0NTg4NQ==","avatar_url":"https://avatars0.githubusercontent.com/u/745885?v=4","gravatar_id":"","url":"https://api.github.com/users/pvannierop","html_url":"https://github.com/pvannierop","followers_url":"https://api.github.com/users/pvannierop/followers","following_url":"https://api.github.com/users/pvannierop/following{/other_user}","gists_url":"https://api.github.com/users/pvannierop/gists{/gist_id}","starred_url":"https://api.github.com/users/pvannierop/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pvannierop/subscriptions","organizations_url":"https://api.github.com/users/pvannierop/orgs","repos_url":"https://api.github.com/users/pvannierop/repos","events_url":"https://api.github.com/users/pvannierop/events{/privacy}","received_events_url":"https://api.github.com/users/pvannierop/received_events","type":"User","site_admin":false},"body":"# What? Why?\r\nThis PR will implement handling of the new `treatment response` (genetic entity) data type by the PlotsTab component. A new plot type _Watefall plot_ is added.\r\n\r\n## Changes\r\n- `Treatment` is shown in data type select boxes of the horz. and vert. axis menu's (when available in cBioPortal db). When selected treatment response genetic profiles are shown in the data source select menu's (see Fig.1). Only treatments selected in the oncoprint heatmap menu are available for selection. \r\n- Treatment data points can be _limited_ (real value lies beyond a certain value) which can be indicated by `>` or `<` prefixes to values (for example _>8.00_, see [this backend PR](https://github.com/cBioPortal/cbioportal/pull/5460)). Bar, scatter and waterfall (see below) plot types contain a legend option `Limit Value` when one or more data points in the plot are limited. Enabling this legend option represents limited data points as diamonds (see Fig.1). This option is enabled by default and is re-enabled after each axis menu change. When __enabled__ limited data values are __excluded__ from calculations of correlation coefficients in the scatter plot legend. \r\n- When `Treatment` data type is selected a `--`option is shown in the other data type menu that represents no data type selected for the corresponding axis (see Fig.1). For treatment data the `Apply log scale` option is displayed in the axis menu's. When the `Treatment` and `--` combination is selected by the user, a new plot type `Waterfall plot` is displayed.\r\n- A new plot type `Waterfall plot` is implemented (see Fig.2). This plot type represents a sorted (asc or desc) bar graph of response values expressed relative to a given threshold value a.k.a. `pivot_threshold `. The `pivot_threshold` is set on a profile level scope and is passed from the cbioportal backend. When no `pivot_threshold` is passed unmodified values are represented. When a waterfall plot is shown `Log-scale` and `Sort Order` controls are shown in the corresponding axis menu that control log10-transformation and asc-desc sorting, respectively. The legend options for this plot type include a new gene selection box that controls for which gene the mutation or CNA information is represented in the plot. For the waterfall plot the mutation and CNA styling options are mutually exclusive. The selected gene is represented in the title of the plot. When legend option `Limit Value` is enabled limited data points are marked by a black diamond above respective bars. Sample and mutation queries are represented by red plus signs below respective bars. The width of the waterfall plot is dynamic with a max-width of 1000px. Download of waterfall plot data includes raw and `pivot_threshold`-adjusted values and the sort order.\r\n\r\n### Notes\r\n- Because PlotsTab only shows treatments selected in Oncoprint functionality in this PR for treatment response data is dependent on [this PR](https://github.com/cBioPortal/cbioportal-frontend/pull/2054) that implements functionality for treatment response data in the OncoprintTab. For review of the Plotstab functionality a treatment list must be added to the URL (f.i. http://localhost:8081/cbioportal/results/plots? ... &treatment_list=**17-AAG**%3B**AEW541**).\r\n\r\n## Images\r\n### Figure 1\r\n1. Treatment data type\r\n2. `--` data type option in other menu\r\n3. `Limit Value` legend option\r\n4. Limited data points styled as diamonds\r\n5. `Log scale` control for treatment profile values\r\n\r\n![Screenshot from 2019-04-04 09-32-03](https://user-images.githubusercontent.com/745885/55537535-b7436b00-56bc-11e9-9562-2c7d5b47b01b.png)\r\n\r\n### Figure 2\r\n1. Waterfall plot (at max width)\r\n2. `Limit Value` legend option\r\n3. Limited data points styled as diamonds above bars\r\n4. Gene selection box for mutation or CNA styling\r\n5. Selected gene represented in title\r\n6. `Log Scale` and `Sort Order` controls for treatment profile values\r\n7. Sample search as red plus sign\r\n\r\n![Screenshot from 2019-04-04 09-32-51](https://user-images.githubusercontent.com/745885/55537543-bd394c00-56bc-11e9-855a-59d801e158bd.png)","created_at":"2019-02-20T14:49:13Z","updated_at":"2019-04-19T08:54:17Z","closed_at":null,"merged_at":null,"merge_commit_sha":"fefaac9857f080d4cbea152dd52a2817c68901b2","assignee":{"login":"adamabeshouse","id":636232,"node_id":"MDQ6VXNlcjYzNjIzMg==","avatar_url":"https://avatars1.githubusercontent.com/u/636232?v=4","gravatar_id":"","url":"https://api.github.com/users/adamabeshouse","html_url":"https://github.com/adamabeshouse","followers_url":"https://api.github.com/users/adamabeshouse/followers","following_url":"https://api.github.com/users/adamabeshouse/following{/other_user}","gists_url":"https://api.github.com/users/adamabeshouse/gists{/gist_id}","starred_url":"https://api.github.com/users/adamabeshouse/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/adamabeshouse/subscriptions","organizations_url":"https://api.github.com/users/adamabeshouse/orgs","repos_url":"https://api.github.com/users/adamabeshouse/repos","events_url":"https://api.github.com/users/adamabeshouse/events{/privacy}","received_events_url":"https://api.github.com/users/adamabeshouse/received_events","type":"User","site_admin":false},"assignees":[{"login":"adamabeshouse","id":636232,"node_id":"MDQ6VXNlcjYzNjIzMg==","avatar_url":"https://avatars1.githubusercontent.com/u/636232?v=4","gravatar_id":"","url":"https://api.github.com/users/adamabeshouse","html_url":"https://github.com/adamabeshouse","followers_url":"https://api.github.com/users/adamabeshouse/followers","following_url":"https://api.github.com/users/adamabeshouse/following{/other_user}","gists_url":"https://api.github.com/users/adamabeshouse/gists{/gist_id}","starred_url":"https://api.github.com/users/adamabeshouse/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/adamabeshouse/subscriptions","organizations_url":"https://api.github.com/users/adamabeshouse/orgs","repos_url":"https://api.github.com/users/adamabeshouse/repos","events_url":"https://api.github.com/users/adamabeshouse/events{/privacy}","received_events_url":"https://api.github.com/users/adamabeshouse/received_events","type":"User","site_admin":false}],"requested_reviewers":[],"requested_teams":[],"labels":[],"milestone":null,"commits_url":"https://api.github.com/repos/cBioPortal/cbioportal-frontend/pulls/2055/commits","review_comments_url":"https://api.github.com/repos/cBioPortal/cbioportal-frontend/pulls/2055/comments","review_comment_url":"https://api.github.com/repos/cBioPortal/cbioportal-frontend/pulls/comments{/number}","comments_url":"https://api.github.com/repos/cBioPortal/cbioportal-frontend/issues/2055/comments","statuses_url":"https://api.github.com/repos/cBioPortal/cbioportal-frontend/statuses/d873c174a4ad84425d34b83d14655bd155d4facc","head":{"label":"thehyve:treatment_response_feature_plotstab","ref":"treatment_response_feature_plotstab","sha":"d873c174a4ad84425d34b83d14655bd155d4facc","user":{"login":"thehyve","id":1502440,"node_id":"MDEyOk9yZ2FuaXphdGlvbjE1MDI0NDA=","avatar_url":"https://avatars3.githubusercontent.com/u/1502440?v=4","gravatar_id":"","url":"https://api.github.com/users/thehyve","html_url":"https://github.com/thehyve","followers_url":"https://api.github.com/users/thehyve/followers","following_url":"https://api.github.com/users/thehyve/following{/other_user}","gists_url":"https://api.github.com/users/thehyve/gists{/gist_id}","starred_url":"https://api.github.com/users/thehyve/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/thehyve/subscriptions","organizations_url":"https://api.github.com/users/thehyve/orgs","repos_url":"https://api.github.com/users/thehyve/repos","events_url":"https://api.github.com/users/thehyve/events{/privacy}","received_events_url":"https://api.github.com/users/thehyve/received_events","type":"Organization","site_admin":false},"repo":{"id":92735261,"node_id":"MDEwOlJlcG9zaXRvcnk5MjczNTI2MQ==","name":"cbioportal-frontend","full_name":"thehyve/cbioportal-frontend","private":false,"owner":{"login":"thehyve","id":1502440,"node_id":"MDEyOk9yZ2FuaXphdGlvbjE1MDI0NDA=","avatar_url":"https://avatars3.githubusercontent.com/u/1502440?v=4","gravatar_id":"","url":"https://api.github.com/users/thehyve","html_url":"https://github.com/thehyve","followers_url":"https://api.github.com/users/thehyve/followers","following_url":"https://api.github.com/users/thehyve/following{/other_user}","gists_url":"https://api.github.com/users/thehyve/gists{/gist_id}","starred_url":"https://api.github.com/users/thehyve/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/thehyve/subscriptions","organizations_url":"https://api.github.com/users/thehyve/orgs","repos_url":"https://api.github.com/users/thehyve/repos","events_url":"https://api.github.com/users/thehyve/events{/privacy}","received_events_url":"https://api.github.com/users/thehyve/received_events","type":"Organization","site_admin":false},"html_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