RFC69 : survival chart with landmark events and hazard ratio #4740

TJMKuijpers · 2023-09-21T14:08:09Z

RFC69: Add hazard ratio and landmarks in the survival plot

For clinical trials, it is customary to report hazard ratios and/or landmark values in survival plots. Currently, survival plots rendered by cBioPortal do not show hazard ratio or landmark information.

This PR is the implementation of RFC69. The new survival chart can be activated by setting &featureFlag=SURVIVAL_PLOT_EXTENDED.

Implemented functions

Number at risk
Most scientific papers show a survival plot together with the number at risk table. We have added this option to the survival plot and show the number of risks below the figure (number at risk at every tick on the x-axis).

Landmark lines

The user activates the landmarks option via a checkbox (by default, the landmark input field is disabled). The user can add values (comma or space separated) that are translated into vertical lines (dashed) in the survival plot.

Underneath the number at risk table, we show a new table with the percentage of patients at that specific landmark point.

Hazard ratios

The user activates the hazard ratio option via a checkbox. The user selects the Control group to serve as a reference (denominator) in the hazard ratio by dragging the Control group to the leftmost position in the Groups menu section. The hazard ratios for each experimental group ( with a 95% confidence interval and p-value) appear below the respective entries in the plot legend.

Implemented tests

Unit test for the new functions

Test for the hazard ratio calculations (based on the survival R package for the ground truth)
Test for the log-rank test to calculate the lower and upper confidence intervals (based on the survival R package)

Implemented screenshot tests:

Survival chart with hazard ratio table and landmark line disabled
Survival chart with landmark event at time point 20
Survival chart with hazard ratio table
Survival chart with hazard ratio table and landmark event at time point 20

TJMKuijpers · 2023-09-21T14:58:56Z

src/shared/lib/comparison/ComparisonStore.ts

@@ -133,7 +133,7 @@ export default abstract class ComparisonStore extends AnalysisStore
    @observable public adjustForLeftTruncation = true;

    constructor(
-        protected appStore: AppStore,
+        public appStore: AppStore,


This one should be made protected again and the featureFlag for the extended survival plot should be shared with in a better way.

src/pages/groupComparison/GroupComparisonUtils.tsx

alisman · 2023-09-27T14:18:29Z

src/pages/groupComparison/Survival.tsx

@@ -317,6 +319,7 @@ export default class Survival extends React.Component<ISurvivalProps, {}> {
                            style={{ paddingBottom: 0 }}
                        >
                            {getStatisticalCautionInfo()}
+                            {getHazardRatioCautionInfo()}


maybe do the same for getStatisticalCautionInfo while we're at it. (Function component)

Also changed it for getStatisticalCautionInfo and also updated /groupComparison/ClinicalData.tsx since it also calls getStatisticalCautionInfo

src/pages/resultsView/survival/hazardRatioGroundTruth.r

alisman · 2023-09-27T14:28:46Z

src/pages/resultsView/survival/logRankTest.ts

+        return _.sortBy(curveData, d => d.months);
+    });
+
+    const groupsTte = sortedCurves.map(curveData => {


can you improve this name? No idea what Tte means. Ir Ev.

alisman · 2023-09-27T15:10:22Z

src/pages/resultsView/survival/logRankTest.ts

+    controlGroup: string,
+    ...survivalCurves: SurvivalCurveItem[][]
+) {
+    const allEvents = _.sortBy(_.flatten(survivalCurves), s => s.months);


this is important business logic here so comments about what we're doing would be helpful to devs trying to understand the basics

alisman · 2023-09-27T15:11:41Z

src/pages/resultsView/survival/SurvivalChartExtended.tsx

+    @computed get tableRowsHazardRatio() {
+        if (this.hazardRatioGroups !== null) {
+            return (
+                <React.Fragment>


i don't think you need Fragment here since you are just returning a single element (table)

Removed the <React.Fragment>

alisman · 2023-09-27T15:15:54Z

src/pages/resultsView/survival/SurvivalChartExtended.tsx

+const SURVIVAL_DOWN_SAMPLING_THRESHOLD = 1000;
+
+@observer
+export default class SurvivalChartExtended


we should discuss reason for doing this as extension rather than just a new component. the "Extension" kind of hides the true nature of this component. lets discuss.

alisman · 2023-10-04T15:56:28Z

@pvannierop I wanted to open a discussion about the practice here of copying an existing component in order to "extend it". Based on discussion with @TJMKuijpers, I now think I understand that <SurvivalExtended> is intended to fully replace <SurvivalChart> and so it's not really an "extension." It's just adding to adding to the existing component (right?). The issue then is that by copying the component in order to work on it, we leave ourselves vulnerable to losing concurrent edits to the original component. If we want to use a feature flag to introduce this work then I think it should be be done via "mode" of the original component. Alternatively, we don't use a feature flag in this case. We just keep the feature branch open. Since this is a pretty isolated feature, I don't see a big cost to that.

Added the input field that reacts on user defined input Implemented multiple landmark lines Add the group information as label below chart landmark line functionality complete Dynamic calculation of groups for axis Implemented hazard ratio updated survival chart and tests show hazard ratio between every group Updated test Updated number at risk and legend Updated styling Updated statistics in survival chart updated CI calculations Updated SV plot Updated styling labels Added feature flag updated files fix behavior disable landmark input updated hazard ratio table style updated style table Updated screenshot tests for extended survival chart removed console.log getStatisticalCautionInfo and getHazardRatioCautionInfo changed to functional component Updated PR Updated legend style for hazard ratio legend Remove hazard ratio warning when feature flag is disabled Run Prettier Update the border chart for the default survival chart Removed feature flag for survival chart Updated screenshots Updated padding to fix screenshot Decreased whitespace between table and figure Update reference screenshot update localdb screenshots ref Updated font family landmark line labels Updated the test for survival chart localdb tests

TJMKuijpers · 2023-10-13T17:08:42Z

@inodb updated the labels for the landmark line groups (had to change CBIOPORTAL_VICTORY_THEME.chart.fontFamily, to CBIOPORTAL_VICTORY_THEME.legend.style.labels.fontFamily). Also updated the reference screenshots so the surival chart tests should pass.

Add the group information as label below chart landmark line functionality Dynamic calculation of groups for axis Implement hazard ratio show hazard ratio between every group Remove hazard ratio warning when feature flag is disabled Removed feature flag for survival chart

inodb requested review from alisman and dippindots September 21, 2023 14:40

TJMKuijpers commented Sep 21, 2023

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TJMKuijpers marked this pull request as ready for review September 25, 2023 07:51

alisman reviewed Sep 27, 2023

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src/pages/groupComparison/GroupComparisonUtils.tsx Outdated Show resolved Hide resolved

alisman reviewed Sep 27, 2023

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src/pages/resultsView/survival/hazardRatioGroundTruth.r Show resolved Hide resolved

TJMKuijpers added the enhancement label Sep 27, 2023

alisman reviewed Sep 27, 2023

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TJMKuijpers force-pushed the survival-plot-landmarks branch 7 times, most recently from 987a847 to ef59d55 Compare October 13, 2023 14:51

TJMKuijpers force-pushed the survival-plot-landmarks branch from afcbd50 to a2f223e Compare October 13, 2023 16:17

inodb added feature and removed enhancement labels Oct 16, 2023

inodb merged commit 2e24485 into cBioPortal:master Oct 16, 2023

dippindots mentioned this pull request Oct 19, 2023

Add download data and PDF option #4757

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RFC69 : survival chart with landmark events and hazard ratio #4740

RFC69 : survival chart with landmark events and hazard ratio #4740

TJMKuijpers commented Sep 21, 2023

TJMKuijpers Sep 21, 2023

alisman Sep 27, 2023

TJMKuijpers Sep 28, 2023

alisman Sep 27, 2023

alisman Sep 27, 2023

alisman Sep 27, 2023

TJMKuijpers Sep 28, 2023

alisman Sep 27, 2023

alisman commented Oct 4, 2023

TJMKuijpers commented Oct 13, 2023

RFC69 : survival chart with landmark events and hazard ratio #4740

RFC69 : survival chart with landmark events and hazard ratio #4740

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TJMKuijpers commented Sep 21, 2023

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alisman commented Oct 4, 2023

TJMKuijpers commented Oct 13, 2023