taxonium-component/dist/WiggleClusterDialog-D_xrwA7d.js

React component for exploring large phylogenetic trees in the browser

import { jsxs as s, Fragment as F, jsx as e } from "react/jsx-runtime";
import { useState as i, useEffect as U } from "react";
import { o as D, u, D as O, B as c, T as E, c as L, O as j, a as R, d as I, t as z, j as G, m as K, aM as B, aN as Q } from "./JBrowsePanel-BNE3gNW1.js";
import { R as H } from "./RadioGroup-VjVK5G6V.js";
import { F as V } from "./FormControlLabel-CfHqydvH.js";
import { R as N } from "./Radio-Bf0n3fp_.js";
const X = D(function({ model: n, children: l, handleClose: o }) {
  const [h, g] = i(""), [v, d] = i(), [x, y] = i(!1), [f, k] = i(""), [m, b] = i(!1), [P, M] = u.useLocalStorage("cluster-samplesPerPixel", "1");
  return s(F, { children: [s(O, { children: [l, s("div", { style: { marginTop: 50 }, children: [e(c, { variant: "contained", onClick: () => {
    b(!m);
  }, children: m ? "Hide advanced options" : "Show advanced options" }), m ? s("div", { style: { marginTop: 20 }, children: [e(E, { children: "This procedure samples the data at each 'pixel' across the visible by default" }), e(L, { label: "Samples per pixel (>1 for denser sampling, between 0-1 for sparser sampling)", variant: "outlined", size: "small", value: P, onChange: (a) => {
    M(a.target.value);
  } })] }) : null] }), s("div", { children: [x ? s("div", { style: { padding: 50 }, children: [e("span", { children: h || "Loading..." }), e(c, { onClick: () => {
    j.stopStopToken(f);
  }, children: "Stop" })] }) : null, v ? e(R.ErrorMessage, { error: v }) : null] })] }), s(I, { children: [e(c, { variant: "contained", disabled: x, onClick: async () => {
    try {
      d(void 0), g("Initializing"), y(!0);
      const a = u.getContainingView(n);
      if (!a.initialized)
        return;
      const { rpcManager: C } = u.getSession(n), { sourcesWithoutLayout: w, adapterConfig: S } = n;
      if (w) {
        const T = z.getRpcSessionId(n), t = j.createStopToken();
        k(t);
        const r = await C.call(T, "MultiWiggleClusterScoreMatrix", {
          regions: a.dynamicBlocks.contentBlocks,
          sources: w,
          sessionId: T,
          adapterConfig: S,
          stopToken: t,
          bpPerPx: a.bpPerPx / +P,
          statusCallback: (p) => {
            g(p);
          }
        });
        n.setLayout(r.order.map((p) => {
          const A = w[p];
          if (!A)
            throw new Error(`out of bounds at ${p}`);
          return A;
        }));
      }
      o();
    } catch (a) {
      !u.isAbortException(a) && G(n) && (console.error(a), d(a));
    } finally {
      y(!1), g(""), k("");
    }
  }, children: "Run clustering" }), e(c, { variant: "contained", color: "secondary", onClick: () => {
    o(), f && j.stopStopToken(f);
  }, children: "Cancel" })] })] });
}), Y = K()((n) => ({
  textAreaFont: {
    fontFamily: "Courier New"
  },
  mgap: {
    display: "flex",
    flexDirection: "column",
    gap: n.spacing(4)
  }
})), Z = D(function({ model: n, handleClose: l, children: o }) {
  const { classes: h } = Y(), [g, v] = i(""), [d, x] = i(), [y, f] = i(), [k, m] = i(!1), [b, P] = u.useLocalStorage("cluster-showAdvanced", !1), [M, a] = i("single"), [C, w] = i("1");
  U(() => {
    (async () => {
      try {
        f(void 0), x(void 0), m(!0);
        const t = u.getContainingView(n), { dynamicBlocks: r, bpPerPx: p } = t, { rpcManager: A } = u.getSession(n), { sourcesWithoutLayout: _, adapterConfig: q } = n, W = z.getRpcSessionId(n), J = await A.call(W, "MultiWiggleGetScoreMatrix", {
          regions: r.contentBlocks,
          sources: _,
          sessionId: W,
          adapterConfig: q,
          bpPerPx: p / +C
        });
        x(J);
      } catch (t) {
        !u.isAbortException(t) && G(n) && (console.error(t), f(t));
      } finally {
        m(!1);
      }
    })();
  }, [n, C]);
  const S = d ? `inputMatrix<-matrix(c(${Object.values(d).map((t) => t.join(",")).join(`,
`)}
),nrow=${Object.values(d).length},byrow=TRUE)
rownames(inputMatrix)<-c(${Object.keys(d).map((t) => `'${t}'`).join(",")})
resultClusters<-hclust(dist(inputMatrix), method='${M}')
cat(resultClusters$order,sep='\\n')` : void 0, T = d ? Object.entries(d).map(([t, r]) => [t, ...r].join("	")).join(`
`) : void 0;
  return s(F, { children: [s(O, { children: [o, s("div", { style: { marginTop: 50 }, children: [s("div", { children: [s("div", { style: {
    display: "flex",
    gap: "8px",
    flexWrap: "wrap",
    marginBottom: "16px"
  }, children: [e(c, { variant: "contained", onClick: () => {
    B.saveAs(new Blob([S || ""], {
      type: "text/plain;charset=utf-8"
    }), "cluster.R");
  }, children: "Download Rscript" }), " ", "or", " ", e(c, { variant: "contained", onClick: () => {
    Q(S || "");
  }, children: "Copy Rscript to clipboard" }), " ", "or", " ", e(c, { variant: "contained", onClick: () => {
    B.saveAs(new Blob([T || ""], {
      type: "text/plain;charset=utf-8"
    }), "scores.tsv");
  }, children: "Download TSV" })] }), e("div", { children: e(c, { variant: "contained", onClick: () => {
    P(!b);
  }, children: b ? "Hide advanced options" : "Show advanced options" }) }), b ? s("div", { children: [e(E, { variant: "h6", children: "Advanced options" }), e(H, { children: Object.entries({
    single: "Single",
    complete: "Complete"
  }).map(([t, r]) => e(V, { control: e(N, { checked: M === t, onChange: () => {
    a(t);
  } }), label: r }, t)) }), s("div", { style: { marginTop: 20 }, children: [e(E, { children: "This procedure samples the data at each 'pixel' across the visible by default" }), e(L, { label: "Samples per pixel (>1 for denser sampling, between 0-1 for sparser sampling)", variant: "outlined", size: "small", value: C, onChange: (t) => {
    w(t.target.value);
  } })] })] }) : null, S ? e("div", {}) : k ? e(R.LoadingEllipses, { variant: "h6", title: "Generating score matrix" }) : y ? e(R.ErrorMessage, { error: y }) : null] }), s("div", { children: [e(E, { variant: "subtitle2", gutterBottom: !0, style: { marginTop: "16px" }, children: "Clustering Results:" }), e(L, { multiline: !0, fullWidth: !0, variant: "outlined", placeholder: "Paste results from Rscript here (sequence of numbers, one per line, specifying the new ordering)", rows: 10, value: g, onChange: (t) => {
    v(t.target.value);
  }, slotProps: {
    input: {
      classes: {
        input: h.textAreaFont
      }
    }
  } })] })] })] }), s(I, { children: [e(c, { variant: "contained", onClick: () => {
    const { sourcesWithoutLayout: t } = n;
    if (t)
      try {
        n.setLayout(g.split(`
`).map((r) => r.trim()).filter((r) => !!r).map((r) => +r).map((r) => {
          const p = t[r - 1];
          if (!p)
            throw new Error(`out of bounds at ${r}`);
          return p;
        }));
      } catch (r) {
        console.error(r), u.getSession(n).notifyError(`${r}`, r);
      }
    l();
  }, children: "Apply clustering" }), e(c, { variant: "contained", color: "secondary", onClick: () => {
    l();
  }, children: "Cancel" })] })] });
});
function $({ activeMode: n, setActiveMode: l }) {
  return e("div", { children: e(H, { children: Object.entries({
    auto: e("div", { children: "Run in-app clustering (slower, particularly for large numbers of samples, uses JS implementation of hclust)" }),
    manual: e("div", { children: "Download R script to run clustering (faster, uses R implementation of hclust)" })
  }).map(([o, h]) => e(V, { control: e(N, { checked: n === o, onChange: () => {
    l(o);
  } }), label: h }, o)) }) });
}
const ie = D(function({ model: n, handleClose: l }) {
  const [o, h] = i("auto");
  return e(R.Dialog, { open: !0, title: "Cluster by score", maxWidth: "xl", onClose: (g, v) => {
    v !== "backdropClick" && l();
  }, children: o === "auto" ? e(X, { model: n, handleClose: l, children: e($, { activeMode: o, setActiveMode: h }) }) : e(Z, { model: n, handleClose: l, children: e($, { activeMode: o, setActiveMode: h }) }) });
});
export {
  ie as default
};
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