@jbrowse/plugin-wiggle 3.1.0 → 3.2.0

package/dist/MultiLinearWiggleDisplay/components/ClusterDialog.js

@@ -1,115 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = ClusterDialog;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const ui_1 = require("@jbrowse/core/ui");
-const util_1 = require("@jbrowse/core/util");
-const tracks_1 = require("@jbrowse/core/util/tracks");
-const material_1 = require("@mui/material");
-const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
-const file_saver_1 = require("file-saver");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const mui_1 = require("tss-react/mui");
-const useStyles = (0, mui_1.makeStyles)()(theme => ({
-    textAreaFont: {
-        fontFamily: 'Courier New',
-    },
-    mgap: {
-        display: 'flex',
-        flexDirection: 'column',
-        gap: theme.spacing(4),
-    },
-}));
-function ClusterDialog({ model, handleClose, }) {
-    const { classes } = useStyles();
-    const [results, setResults] = (0, react_1.useState)();
-    const [error, setError] = (0, react_1.useState)();
-    const [paste, setPaste] = (0, react_1.useState)('');
-    const [useCompleteMethod, setUseCompleteMethod] = (0, react_1.useState)(false);
-    (0, react_1.useEffect)(() => {
-        ;
-        (async () => {
-            try {
-                setError(undefined);
-                const view = (0, util_1.getContainingView)(model);
-                if (!view.initialized) {
-                    return;
-                }
-                const { rpcManager } = (0, util_1.getSession)(model);
-                const { sources, minorAlleleFrequencyFilter, adapterConfig } = model;
-                const sessionId = (0, tracks_1.getRpcSessionId)(model);
-                const { bpPerPx } = view;
-                const ret = (await rpcManager.call(sessionId, 'MultiWiggleGetScoreMatrix', {
-                    regions: view.dynamicBlocks.contentBlocks,
-                    sources,
-                    minorAlleleFrequencyFilter,
-                    sessionId,
-                    adapterConfig,
-                    bpPerPx,
-                }));
-                const entries = Object.values(ret);
-                const keys = Object.keys(ret);
-                const clusterMethod = useCompleteMethod ? 'complete' : 'single';
-                const text = `try(library(fastcluster), silent=TRUE)
-inputMatrix<-matrix(c(${entries.map(val => val.scores.join(',')).join(',\n')}
-),nrow=${entries.length},byrow=TRUE)
-rownames(inputMatrix)<-c(${keys.map(key => `'${key}'`).join(',')})
-resultClusters<-hclust(dist(inputMatrix), method='${clusterMethod}')
-cat(resultClusters$order,sep='\\n')`;
-                setResults(text);
-            }
-            catch (e) {
-                if (!(0, util_1.isAbortException)(e) && (0, mobx_state_tree_1.isAlive)(model)) {
-                    console.error(e);
-                    setError(e);
-                }
-            }
-        })();
-    }, [model, useCompleteMethod]);
-    return ((0, jsx_runtime_1.jsxs)(ui_1.Dialog, { open: true, title: "Cluster by score", onClose: handleClose, children: [(0, jsx_runtime_1.jsx)(material_1.DialogContent, { children: (0, jsx_runtime_1.jsxs)("div", { className: classes.mgap, children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "This page will produce an R script that will perform hierarchical clustering on the visible score data using `hclust`." }), (0, jsx_runtime_1.jsx)(material_1.Typography, { children: "You can then paste the results in this form to specify the row ordering." }), results ? ((0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsxs)("div", { children: ["Step 1:", ' ', (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
-                                            (0, file_saver_1.saveAs)(new Blob([results || ''], {
-                                                type: 'text/plain;charset=utf-8',
-                                            }), 'cluster.R');
-                                        }, children: "Download Rscript" }), ' ', "or", ' ', (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
-                                            (0, copy_to_clipboard_1.default)(results || '');
-                                        }, children: "Copy Rscript to clipboard" }), (0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { control: (0, jsx_runtime_1.jsx)(material_1.Checkbox, { checked: useCompleteMethod, onChange: e => {
-                                                setUseCompleteMethod(e.target.checked);
-                                            } }), label: "Use 'complete' linkage method instead of 'single'" }), (0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(material_1.TextField, { multiline: true, fullWidth: true, variant: "outlined", placeholder: "Step 2. Paste results from Rscript here (sequence of numbers, one per line, specifying the new ordering)", rows: 10, value: paste, onChange: event => {
-                                                setPaste(event.target.value);
-                                            }, slotProps: {
-                                                input: {
-                                                    classes: {
-                                                        input: classes.textAreaFont,
-                                                    },
-                                                },
-                                            } }) })] }) })) : ((0, jsx_runtime_1.jsx)(ui_1.LoadingEllipses, { variant: "h6", title: "Generating score matrix" })), error ? (0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: error }) : null] }) }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { disabled: !results, variant: "contained", onClick: () => {
-                            const { sources } = model;
-                            if (sources) {
-                                try {
-                                    model.setLayout(paste
-                                        .split('\n')
-                                        .map(t => t.trim())
-                                        .filter(f => !!f)
-                                        .map(r => +r)
-                                        .map(idx => {
-                                        const ret = sources[idx - 1];
-                                        if (!ret) {
-                                            throw new Error(`out of bounds at ${idx}`);
-                                        }
-                                        return ret;
-                                    }));
-                                }
-                                catch (e) {
-                                    console.error(e);
-                                    setError(e);
-                                }
-                            }
-                            handleClose();
-                        }, children: "Apply clustering" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
-                            handleClose();
-                        }, children: "Cancel" })] })] }));
-}

package/esm/MultiLinearWiggleDisplay/components/ClusterDialog.d.ts

@@ -1,11 +0,0 @@
-import type { Source } from '../types';
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-export default function ClusterDialog({ model, handleClose, }: {
-    model: {
-        sources?: Source[];
-        minorAlleleFrequencyFilter?: number;
-        adapterConfig: AnyConfigurationModel;
-        setLayout: (arg: Source[]) => void;
-    };
-    handleClose: () => void;
-}): import("react/jsx-runtime").JSX.Element;

package/esm/MultiLinearWiggleDisplay/components/ClusterDialog.js

@@ -1,109 +0,0 @@
-import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
-import { useEffect, useState } from 'react';
-import { Dialog, ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui';
-import { getContainingView, getSession, isAbortException, } from '@jbrowse/core/util';
-import { getRpcSessionId } from '@jbrowse/core/util/tracks';
-import { Button, Checkbox, DialogActions, DialogContent, FormControlLabel, TextField, Typography, } from '@mui/material';
-import copy from 'copy-to-clipboard';
-import { saveAs } from 'file-saver';
-import { isAlive } from 'mobx-state-tree';
-import { makeStyles } from 'tss-react/mui';
-const useStyles = makeStyles()(theme => ({
-    textAreaFont: {
-        fontFamily: 'Courier New',
-    },
-    mgap: {
-        display: 'flex',
-        flexDirection: 'column',
-        gap: theme.spacing(4),
-    },
-}));
-export default function ClusterDialog({ model, handleClose, }) {
-    const { classes } = useStyles();
-    const [results, setResults] = useState();
-    const [error, setError] = useState();
-    const [paste, setPaste] = useState('');
-    const [useCompleteMethod, setUseCompleteMethod] = useState(false);
-    useEffect(() => {
-        ;
-        (async () => {
-            try {
-                setError(undefined);
-                const view = getContainingView(model);
-                if (!view.initialized) {
-                    return;
-                }
-                const { rpcManager } = getSession(model);
-                const { sources, minorAlleleFrequencyFilter, adapterConfig } = model;
-                const sessionId = getRpcSessionId(model);
-                const { bpPerPx } = view;
-                const ret = (await rpcManager.call(sessionId, 'MultiWiggleGetScoreMatrix', {
-                    regions: view.dynamicBlocks.contentBlocks,
-                    sources,
-                    minorAlleleFrequencyFilter,
-                    sessionId,
-                    adapterConfig,
-                    bpPerPx,
-                }));
-                const entries = Object.values(ret);
-                const keys = Object.keys(ret);
-                const clusterMethod = useCompleteMethod ? 'complete' : 'single';
-                const text = `try(library(fastcluster), silent=TRUE)
-inputMatrix<-matrix(c(${entries.map(val => val.scores.join(',')).join(',\n')}
-),nrow=${entries.length},byrow=TRUE)
-rownames(inputMatrix)<-c(${keys.map(key => `'${key}'`).join(',')})
-resultClusters<-hclust(dist(inputMatrix), method='${clusterMethod}')
-cat(resultClusters$order,sep='\\n')`;
-                setResults(text);
-            }
-            catch (e) {
-                if (!isAbortException(e) && isAlive(model)) {
-                    console.error(e);
-                    setError(e);
-                }
-            }
-        })();
-    }, [model, useCompleteMethod]);
-    return (_jsxs(Dialog, { open: true, title: "Cluster by score", onClose: handleClose, children: [_jsx(DialogContent, { children: _jsxs("div", { className: classes.mgap, children: [_jsx(Typography, { children: "This page will produce an R script that will perform hierarchical clustering on the visible score data using `hclust`." }), _jsx(Typography, { children: "You can then paste the results in this form to specify the row ordering." }), results ? (_jsx("div", { children: _jsxs("div", { children: ["Step 1:", ' ', _jsx(Button, { variant: "contained", onClick: () => {
-                                            saveAs(new Blob([results || ''], {
-                                                type: 'text/plain;charset=utf-8',
-                                            }), 'cluster.R');
-                                        }, children: "Download Rscript" }), ' ', "or", ' ', _jsx(Button, { variant: "contained", onClick: () => {
-                                            copy(results || '');
-                                        }, children: "Copy Rscript to clipboard" }), _jsx(FormControlLabel, { control: _jsx(Checkbox, { checked: useCompleteMethod, onChange: e => {
-                                                setUseCompleteMethod(e.target.checked);
-                                            } }), label: "Use 'complete' linkage method instead of 'single'" }), _jsx("div", { children: _jsx(TextField, { multiline: true, fullWidth: true, variant: "outlined", placeholder: "Step 2. Paste results from Rscript here (sequence of numbers, one per line, specifying the new ordering)", rows: 10, value: paste, onChange: event => {
-                                                setPaste(event.target.value);
-                                            }, slotProps: {
-                                                input: {
-                                                    classes: {
-                                                        input: classes.textAreaFont,
-                                                    },
-                                                },
-                                            } }) })] }) })) : (_jsx(LoadingEllipses, { variant: "h6", title: "Generating score matrix" })), error ? _jsx(ErrorMessage, { error: error }) : null] }) }), _jsxs(DialogActions, { children: [_jsx(Button, { disabled: !results, variant: "contained", onClick: () => {
-                            const { sources } = model;
-                            if (sources) {
-                                try {
-                                    model.setLayout(paste
-                                        .split('\n')
-                                        .map(t => t.trim())
-                                        .filter(f => !!f)
-                                        .map(r => +r)
-                                        .map(idx => {
-                                        const ret = sources[idx - 1];
-                                        if (!ret) {
-                                            throw new Error(`out of bounds at ${idx}`);
-                                        }
-                                        return ret;
-                                    }));
-                                }
-                                catch (e) {
-                                    console.error(e);
-                                    setError(e);
-                                }
-                            }
-                            handleClose();
-                        }, children: "Apply clustering" }), _jsx(Button, { variant: "contained", color: "secondary", onClick: () => {
-                            handleClose();
-                        }, children: "Cancel" })] })] }));
-}