Risk model: Table 1, each risk group's clinical and genomic makeup

app/lab/kind-cards.tsx

@@ -11,10 +11,13 @@ import { TimelineBody } from "./timeline-body";
 import { AlterationsBody } from "./alterations-body";
 import { Checkbox } from "../_ui/checkbox";
 import { Input } from "../_ui/input";
-import { OptionSelect } from "../_ui/choice.tsx";
+import { Choice, OptionSelect } from "../_ui/choice.tsx";
 import { FIELD } from "../_ui/toolbar.ts";
 import { RISK_LABEL_ABOVE } from "../../lib/figures/riskmodel.ts";
+import { RiskTable1Button } from "./risk-table1-dialog.tsx";
 import { RiskGroupsButton } from "./risk-groups-dialog.tsx";
+import { GearMenu } from "../_ui/gear-menu";
+import { Settings2 } from "lucide-react";
 
 /**
  * A text field that keeps what is being typed to itself and hands the page the value only on
@@ -118,6 +121,37 @@ export interface KindCardCtx {
 
 /** the risk model's covariate menus, open or shut, by view (a viewport state, not the document's) */
 const RISK_MENUS = new Map<string, boolean>();
+/** the runs the model settings offer (OncoCast recommends 50 or more) */
+const RISK_RUN_STEPS = [5, 10, 20, 50];
+const RISK_PENALTIES: [string, string][] = [["1", "lasso"], ["0.5", "elastic net"], ["0.1", "mostly ridge"]];
+
+/**
+ * The risk model's fitting settings, set once and rarely changed, behind the view's settings menu
+ * (the sequence and course views' idiom) so the toolbar keeps to what a reader works with.
+ */
+function RiskModelSettings({ vi, spec, busy, patch }: { vi: number; spec: any; busy: boolean; patch: (p: Record<string, unknown>) => void }) {
+  const alpha = String(spec.alpha ?? 0.5), runs = String(spec.runs ?? 10);
+  const penalties = RISK_PENALTIES.some(([v]) => v === alpha) ? RISK_PENALTIES : [[alpha, "alpha " + alpha] as [string, string], ...RISK_PENALTIES];
+  const runSteps = RISK_RUN_STEPS.map(String);
+  return (
+    <GearMenu menuId={"risk-settings:" + vi} menuStore={RISK_MENUS} wide className="risksettingsbtn" contentClassName="gap-1.5 px-2.5 py-2" title="risk model options"
+      label={<><Settings2 />settings</>}>
+      <div className="setrow" title="the lasso share of the penalty: lasso keeps fewer genes, ridge keeps all of them shrunk">
+        <span className="meta">penalty</span>
+        <Choice className="flex-1" value={alpha} disabled={busy} onChange={(v) => patch({ alpha: Number(v) })} options={penalties} />
+      </div>
+      <div className="setrow" title="random two-thirds / one-third splits; each patient's score is the mean over the runs that held them out (OncoCast recommends 50 or more)">
+        <span className="meta">runs</span>
+        <Choice className="flex-1" value={runs} disabled={busy} onChange={(v) => patch({ runs: Number(v) })}
+          options={(runSteps.includes(runs) ? runSteps : [runs, ...runSteps]).map((r) => [r, r] as const)} />
+      </div>
+      <label className="chk" title="train only on the discovery half of the engine's fixed split, and report the groups, table and C-index on the validation half, which the model never saw">
+        <Checkbox checked={!!spec.validate} disabled={busy} onCheckedChange={(on) => patch({ validate: (on === true) || undefined })} /> validate on held-out half
+      </label>
+    </GearMenu>
+  );
+}
+
 /** the volcano's label thresholds the card offers */
 const RISK_LABEL_STEPS = [0.1, 0.25, 0.5, 0.75, 0.9, 1];
 
@@ -417,8 +451,6 @@ export function KindCardControls({ c }: { c: KindCardCtx }) {
               {cats.map((a) => <option key={a} value={a}>{a}</option>)}
             </OptionSelect>
           </label>
-        </div>
-        <div className="tbz"><span className="tbl">adjust</span>
           <PickMenu label="covariates" title="clinical attributes always kept in the model, never penalised (at most 6): numbers as they are, categories against their commonest value. Prefer an age at diagnosis to an age at last contact, which makes longer survivors look older"
             options={c.attrs.filter((a) => a.attribute !== spec.strata).map((a) => ({ value: a.attribute, label: a.attribute, hint: a.kind === "num" ? "number" : "category" }))}
             chosen={spec.covariates || []} max={6} busy={busy} menuId={"risk-cov:" + c.vi} menuStore={RISK_MENUS}
@@ -443,20 +475,9 @@ export function KindCardControls({ c }: { c: KindCardCtx }) {
           </>}
         </div>
         <div className="tbz"><span className="tbl">model</span>
-          <label className="chk" title="train only on the discovery half of the engine's fixed held-out split, and report the groups, table and C-index on the validation half, which the model never saw">
-            <Checkbox checked={!!spec.validate} disabled={busy} onCheckedChange={(on) => patch({ validate: (on === true) || undefined })} /> validate on held-out half
-          </label>
-          <label className="tbfield" title="the l1 share of the penalty: lasso keeps fewer genes, ridge keeps all of them shrunk">
-            penalty <OptionSelect value={String(spec.alpha ?? 0.5)} disabled={busy} onValueChange={(v) => patch({ alpha: Number(v) })}>
-              <option value="1">lasso</option><option value="0.5">elastic net</option><option value="0.1">mostly ridge</option>
-            </OptionSelect>
-          </label>
-          <label className="tbfield" title="random two-thirds / one-third splits; each patient's score is the mean over the runs that held them out (OncoCast recommends 50 or more)">
-            runs <OptionSelect value={String(spec.runs ?? 10)} disabled={busy} onValueChange={(v) => patch({ runs: Number(v) })}>
-              {[5, 10, 20, 50].map((r) => <option key={r} value={r}>{r}</option>)}
-            </OptionSelect>
-          </label>
+          <RiskModelSettings vi={c.vi} spec={spec} busy={busy} patch={patch} />
           <RiskGroupsButton spec={spec} m={c.v?.riskmodel} busy={busy} onApply={patch} />
+          <RiskTable1Button vi={c.vi} spec={spec} m={c.v?.riskmodel} busy={busy} attrs={c.attrs} docJson={c.docJson} onPatch={patch} />
         </div>
         <div className="tbz"><span className="tbl">view</span>
           <label className="tbfield" title="the volcano names the genes the model kept in at least this share of its runs; the rest are drawn unnamed">

app/lab/risk-groups-dialog.tsx

@@ -32,6 +32,9 @@ const PRESETS: { label: string; g: Groups }[] = [
   { label: "Top 20%", g: { cuts: [80] } }, { label: "Top 10%", g: { cuts: [90] } },
 ];
 
+/** equal-quantile groups by their usual names (the presets' words) */
+const EQUAL_NAMES: Record<number, string> = { 2: "halves (median)", 3: "tertiles", 4: "quartiles", 5: "quintiles" };
+
 /** the view's groups as the dialog holds them: cuts as whole percentiles */
 export function groupsOf(spec: { groups?: number; cuts?: number[] }): Groups {
   return spec.cuts ? { cuts: spec.cuts.map((c) => Math.round(c * 100)) } : { groups: spec.groups ?? 3 };
@@ -47,11 +50,13 @@ export function RiskGroupsButton({ spec, m, busy, onApply }: {
 }) {
   const [open, setOpen] = useState(false);
   const g = groupsOf(spec);
-  const text = "cuts" in g ? "cut at " + g.cuts.join(", ") + "%" : g.groups + " equal groups";
+  // the button is the way in; what the groups are now is drawn in the figure and said in its title
+  const now = "cuts" in g ? "cut at the " + g.cuts.join(", ") + "th percentile" + (g.cuts.length > 1 ? "s" : "") + " of the risk score"
+    : (EQUAL_NAMES[g.groups] ?? g.groups + " equal groups") + ": equal shares of patients by risk score, tied scores kept together";
   return <>
     <Button variant="outline" size="sm" className={TB + " riskgroupsbtn"} disabled={busy || !m}
-      title={!m ? "waiting for the model: the groups are cut from its scores" : "choose where the risk groups are cut"} onClick={() => setOpen(true)}>
-      groups: {text}
+      title={!m ? "waiting for the model: the groups are cut from its scores" : now + " — click to change"} onClick={() => setOpen(true)}>
+      groups
     </Button>
     {open && m && <RiskGroupsDialog m={m} initial={g} onClose={() => setOpen(false)}
       onApply={(next) => { onApply("cuts" in next ? { cuts: next.cuts.map((c) => c / 100), groups: undefined } : { groups: next.groups === 3 ? undefined : next.groups, cuts: undefined }); setOpen(false); }} />}