@sjcrh/proteinpaint-types 2.98.0 → 2.98.1-0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/{chunk-SRDMLS6D.js → chunk-GQVW2DPA.js} +35 -73
- package/dist/{chunk-WCMW6A75.js → chunk-Y4KYTIK6.js} +2 -2
- package/dist/index.js +2 -2
- package/dist/termdb.topVariablyExpressedGenes.js +1 -1
- package/dist/termdb.violin.js +1 -1
- package/package.json +1 -1
- package/src/dataset.ts +18 -13
- package/src/routes/termdb.boxplot.ts +4 -4
- package/src/routes/termdb.violin.ts +3 -6
- package/src/termdb.matrix.ts +14 -13
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@@ -1500,12 +1500,12 @@ var validViolinResponse = (input) => {
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const __is = (input2) => {
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const $join = import_typia.createValidate.join;
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const $io0 = (input3) => "number" === typeof input3.status && "string" === typeof input3.error;
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const $io1 = (input3) => "number" === typeof input3.min && "number" === typeof input3.max && (Array.isArray(input3.plots) && input3.plots.every((elem) => "object" === typeof elem && null !== elem && $io2(elem))) && (void 0 === input3.pvalues || Array.isArray(input3.pvalues) && input3.pvalues.every((elem) => Array.isArray(elem) && elem.every((elem2) => "object" === typeof elem2 && null !== elem2 && false === Array.isArray(elem2) && $
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const $io2 = (input3) => "string" === typeof input3.color && ("object" === typeof input3.density && null !== input3.density && $io3(input3.density)) && true && "string" === typeof input3.label && "number" === typeof input3.plotValueCount && "string" === typeof input3.seriesId && "string" === typeof input3.src && (
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const $io1 = (input3) => "number" === typeof input3.min && "number" === typeof input3.max && (Array.isArray(input3.plots) && input3.plots.every((elem) => "object" === typeof elem && null !== elem && $io2(elem))) && (void 0 === input3.pvalues || Array.isArray(input3.pvalues) && input3.pvalues.every((elem) => Array.isArray(elem) && elem.every((elem2) => "object" === typeof elem2 && null !== elem2 && false === Array.isArray(elem2) && $io6(elem2)))) && (null === input3.uncomputableValues || Array.isArray(input3.uncomputableValues) && input3.uncomputableValues.every((elem) => "object" === typeof elem && null !== elem && false === Array.isArray(elem) && $io7(elem)));
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const $io2 = (input3) => "string" === typeof input3.color && ("object" === typeof input3.density && null !== input3.density && $io3(input3.density)) && true && "string" === typeof input3.label && "number" === typeof input3.plotValueCount && "string" === typeof input3.seriesId && "string" === typeof input3.src && (Array.isArray(input3.summaryStats) && input3.summaryStats.every((elem) => "object" === typeof elem && null !== elem && $io5(elem)));
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const $io3 = (input3) => Array.isArray(input3.bins) && input3.bins.every((elem) => "object" === typeof elem && null !== elem && $io4(elem)) && "number" === typeof input3.densityMax && "number" === typeof input3.densityMin;
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const $io4 = (input3) => "number" === typeof input3.x0 && "number" === typeof input3.x1 && "number" === typeof input3.density;
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const $io5 = (input3) =>
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const $io6 = (input3) =>
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const $io5 = (input3) => "string" === typeof input3.id && "string" === typeof input3.label && "number" === typeof input3.value;
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const $io6 = (input3) => (void 0 === input3.value || "string" === typeof input3.value) && (void 0 === input3.html || "string" === typeof input3.html);
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const $io7 = (input3) => Object.keys(input3).every((key) => {
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const value = input3[key];
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if (void 0 === value)
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@@ -1514,15 +1514,6 @@ var validViolinResponse = (input) => {
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return "number" === typeof value;
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return true;
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});
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const $io8 = (input3) => (void 0 === input3.value || "string" === typeof input3.value) && (void 0 === input3.html || "string" === typeof input3.html);
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const $io9 = (input3) => Object.keys(input3).every((key) => {
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const value = input3[key];
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if (void 0 === value)
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return true;
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if (RegExp(/(.*)/).test(key))
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return "number" === typeof value;
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return true;
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});
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const $iu0 = (input3) => (() => {
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if (void 0 !== input3.status)
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return $io0(input3);
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@@ -1581,7 +1572,7 @@ var validViolinResponse = (input) => {
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path: _path2 + ".pvalues[" + _index2 + "][" + _index3 + "]",
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expected: "PValueEntries",
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value: elem2
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})) && $
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})) && $vo6(elem2, _path2 + ".pvalues[" + _index2 + "][" + _index3 + "]", _exceptionable2) || $report(_exceptionable2, {
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path: _path2 + ".pvalues[" + _index2 + "][" + _index3 + "]",
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expected: "PValueEntries",
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value: elem2
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@@ -1593,22 +1584,22 @@ var validViolinResponse = (input) => {
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path: _path2 + ".pvalues",
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expected: "(Array<Array<PValueEntries>> | undefined)",
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value: input3.pvalues
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}), null === input3.
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path: _path2 + ".
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}), null === input3.uncomputableValues || (Array.isArray(input3.uncomputableValues) || $report(_exceptionable2, {
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path: _path2 + ".uncomputableValues",
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expected: "(Array<__type> | null)",
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value: input3.
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})) && input3.
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path: _path2 + ".
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expected: "__type
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value: input3.uncomputableValues
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})) && input3.uncomputableValues.map((elem, _index4) => ("object" === typeof elem && null !== elem && false === Array.isArray(elem) || $report(_exceptionable2, {
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path: _path2 + ".uncomputableValues[" + _index4 + "]",
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expected: "__type",
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value: elem
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})) && $
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path: _path2 + ".
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expected: "__type
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})) && $vo7(elem, _path2 + ".uncomputableValues[" + _index4 + "]", _exceptionable2) || $report(_exceptionable2, {
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path: _path2 + ".uncomputableValues[" + _index4 + "]",
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expected: "__type",
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value: elem
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})).every((flag) => flag) || $report(_exceptionable2, {
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path: _path2 + ".
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path: _path2 + ".uncomputableValues",
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expected: "(Array<__type> | null)",
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value: input3.
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value: input3.uncomputableValues
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})].every((flag) => flag);
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const $vo2 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.color || $report(_exceptionable2, {
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path: _path2 + ".color",
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@@ -1638,33 +1629,33 @@ var validViolinResponse = (input) => {
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path: _path2 + ".src",
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expected: "string",
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value: input3.src
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}), (
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}), (Array.isArray(input3.summaryStats) || $report(_exceptionable2, {
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path: _path2 + ".summaryStats",
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expected: "
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expected: "Array<ValuesEntries>",
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value: input3.summaryStats
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})) &&
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})) && input3.summaryStats.map((elem, _index5) => ("object" === typeof elem && null !== elem || $report(_exceptionable2, {
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path: _path2 + ".summaryStats[" + _index5 + "]",
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expected: "ValuesEntries",
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value: elem
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})) && $vo5(elem, _path2 + ".summaryStats[" + _index5 + "]", _exceptionable2) || $report(_exceptionable2, {
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path: _path2 + ".summaryStats[" + _index5 + "]",
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expected: "ValuesEntries",
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value: elem
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})).every((flag) => flag) || $report(_exceptionable2, {
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path: _path2 + ".summaryStats",
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expected: "
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expected: "Array<ValuesEntries>",
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value: input3.summaryStats
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}), null === input3.uncomputableValueObj || ("object" === typeof input3.uncomputableValueObj && null !== input3.uncomputableValueObj && false === Array.isArray(input3.uncomputableValueObj) || $report(_exceptionable2, {
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path: _path2 + ".uncomputableValueObj",
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expected: "(__type.o1 | null)",
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value: input3.uncomputableValueObj
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})) && $vo7(input3.uncomputableValueObj, _path2 + ".uncomputableValueObj", _exceptionable2) || $report(_exceptionable2, {
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path: _path2 + ".uncomputableValueObj",
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expected: "(__type.o1 | null)",
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value: input3.uncomputableValueObj
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})].every((flag) => flag);
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const $vo3 = (input3, _path2, _exceptionable2 = true) => [(Array.isArray(input3.bins) || $report(_exceptionable2, {
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path: _path2 + ".bins",
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expected: "Array<BinsEntries>",
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value: input3.bins
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})) && input3.bins.map((elem,
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path: _path2 + ".bins[" +
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})) && input3.bins.map((elem, _index6) => ("object" === typeof elem && null !== elem || $report(_exceptionable2, {
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path: _path2 + ".bins[" + _index6 + "]",
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expected: "BinsEntries",
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value: elem
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})) && $vo4(elem, _path2 + ".bins[" +
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path: _path2 + ".bins[" +
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})) && $vo4(elem, _path2 + ".bins[" + _index6 + "]", _exceptionable2) || $report(_exceptionable2, {
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path: _path2 + ".bins[" + _index6 + "]",
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expected: "BinsEntries",
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value: elem
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})).every((flag) => flag) || $report(_exceptionable2, {
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@@ -1693,24 +1684,7 @@ var validViolinResponse = (input) => {
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expected: "number",
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value: input3.density
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})].every((flag) => flag);
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const $vo5 = (input3, _path2, _exceptionable2 = true) => [
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path: _path2 + ".values",
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expected: "Array<ValuesEntries>",
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value: input3.values
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})) && input3.values.map((elem, _index6) => ("object" === typeof elem && null !== elem || $report(_exceptionable2, {
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path: _path2 + ".values[" + _index6 + "]",
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expected: "ValuesEntries",
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value: elem
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})) && $vo6(elem, _path2 + ".values[" + _index6 + "]", _exceptionable2) || $report(_exceptionable2, {
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path: _path2 + ".values[" + _index6 + "]",
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expected: "ValuesEntries",
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value: elem
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})).every((flag) => flag) || $report(_exceptionable2, {
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path: _path2 + ".values",
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expected: "Array<ValuesEntries>",
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value: input3.values
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})].every((flag) => flag);
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const $vo6 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.id || $report(_exceptionable2, {
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const $vo5 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.id || $report(_exceptionable2, {
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path: _path2 + ".id",
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expected: "string",
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value: input3.id
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expected: "number",
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value: input3.value
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})].every((flag) => flag);
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const $
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const value = input3[key];
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if (void 0 === value)
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return true;
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if (RegExp(/(.*)/).test(key))
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return "number" === typeof value || $report(_exceptionable2, {
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path: _path2 + $join(key),
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expected: "number",
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value
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});
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return true;
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}).every((flag) => flag)].every((flag) => flag);
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const $vo8 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.value || "string" === typeof input3.value || $report(_exceptionable2, {
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const $vo6 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.value || "string" === typeof input3.value || $report(_exceptionable2, {
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path: _path2 + ".value",
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expected: "(string | undefined)",
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value: input3.value
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expected: "(string | undefined)",
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value: input3.html
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})].every((flag) => flag);
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const $
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const $vo7 = (input3, _path2, _exceptionable2 = true) => [false === _exceptionable2 || Object.keys(input3).map((key) => {
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const value = input3[key];
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if (void 0 === value)
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return true;
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@@ -24,7 +24,7 @@ var validTermdbTopVariablyExpressedGenesRequest = (input) => {
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const $join = import_typia.createValidate.join;
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const $io0 = (input3) => "string" === typeof input3.genome && "string" === typeof input3.dslabel && "number" === typeof input3.maxGenes && (void 0 === input3.geneSet || "object" === typeof input3.geneSet && null !== input3.geneSet && $io1(input3.geneSet)) && (void 0 === input3.min_median_log2_uqfpkm || "number" === typeof input3.min_median_log2_uqfpkm) && (void 0 === input3.filter_extreme_values || "number" === typeof input3.filter_extreme_values) && (void 0 === input3.min_count || "number" === typeof input3.min_count) && (void 0 === input3.min_total_count || "number" === typeof input3.min_total_count) && (void 0 === input3.rank_type || "object" === typeof input3.rank_type && null !== input3.rank_type && $io2(input3.rank_type)) && (void 0 === input3.filter || "object" === typeof input3.filter && null !== input3.filter && $io3(input3.filter)) && true;
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const $io1 = (input3) => ("all" === input3.type || "custom" === input3.type || "msigdb" === input3.type) && (null === input3.geneList || Array.isArray(input3.geneList) && input3.geneList.every((elem) => "string" === typeof elem));
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const $io2 = (input3) => "
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const $io2 = (input3) => "iqr" === input3.type || "var" === input3.type;
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const $io3 = (input3) => "lst" === input3.type && (void 0 === input3["in"] || "boolean" === typeof input3["in"]) && ("and" === input3.join || "or" === input3.join) && (void 0 === input3.tag || "string" === typeof input3.tag) && (Array.isArray(input3.lst) && input3.lst.every((elem) => "object" === typeof elem && null !== elem && $iu0(elem)));
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const $io4 = (input3) => (void 0 === input3.join || "string" === typeof input3.join) && (void 0 === input3.isnot || "boolean" === typeof input3.isnot) && ("object" === typeof input3.term && null !== input3.term && $io5(input3.term)) && (void 0 === input3.groupset_label || "string" === typeof input3.groupset_label) && (Array.isArray(input3.values) && input3.values.every((elem) => "object" === typeof elem && null !== elem && false === Array.isArray(elem) && $io7(elem)));
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const $io5 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "categorical" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io6(input3.values)) && ("object" === typeof input3.groupsetting && null !== input3.groupsetting && $iu4(input3.groupsetting));
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value: input3.geneList
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const $vo2 = (input3, _path2, _exceptionable2 = true) => ["
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const $vo2 = (input3, _path2, _exceptionable2 = true) => ["iqr" === input3.type || "var" === input3.type || $report(_exceptionable2, {
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package/dist/index.js
CHANGED
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termdbTopVariablyExpressedGenesPayload,
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validTermdbTopVariablyExpressedGenesRequest,
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4
4
|
validTermdbTopVariablyExpressedGenesResponse
|
|
5
|
-
} from "./chunk-
|
|
5
|
+
} from "./chunk-Y4KYTIK6.js";
|
|
6
6
|
import {
|
|
7
7
|
validViolinRequest,
|
|
8
8
|
validViolinResponse,
|
|
9
9
|
violinPayload
|
|
10
|
-
} from "./chunk-
|
|
10
|
+
} from "./chunk-GQVW2DPA.js";
|
|
11
11
|
import {
|
|
12
12
|
tilePayload,
|
|
13
13
|
validTileRequest,
|
|
@@ -2,7 +2,7 @@ import {
|
|
|
2
2
|
termdbTopVariablyExpressedGenesPayload,
|
|
3
3
|
validTermdbTopVariablyExpressedGenesRequest,
|
|
4
4
|
validTermdbTopVariablyExpressedGenesResponse
|
|
5
|
-
} from "./chunk-
|
|
5
|
+
} from "./chunk-Y4KYTIK6.js";
|
|
6
6
|
import "./chunk-Z6B6IQIY.js";
|
|
7
7
|
export {
|
|
8
8
|
termdbTopVariablyExpressedGenesPayload,
|
package/dist/termdb.violin.js
CHANGED
package/package.json
CHANGED
package/src/dataset.ts
CHANGED
|
@@ -951,6 +951,15 @@ type SurvivalSettings = {
|
|
|
951
951
|
xTickValues?: number[]
|
|
952
952
|
}
|
|
953
953
|
|
|
954
|
+
type RegressionSettings = {
|
|
955
|
+
/** disable interactions */
|
|
956
|
+
disableInteractions?: boolean
|
|
957
|
+
/** hide type III statistics table in results */
|
|
958
|
+
hideType3?: boolean
|
|
959
|
+
/** hide statistical tests table in results */
|
|
960
|
+
hideTests?: boolean
|
|
961
|
+
}
|
|
962
|
+
|
|
954
963
|
type MatrixSettings = {
|
|
955
964
|
maxSample?: number
|
|
956
965
|
svgCanvasSwitch?: number
|
|
@@ -1021,6 +1030,11 @@ type Survival = {
|
|
|
1021
1030
|
settings?: SurvivalSettings
|
|
1022
1031
|
}
|
|
1023
1032
|
|
|
1033
|
+
type Regression = {
|
|
1034
|
+
/** default settings for regression */
|
|
1035
|
+
settings?: RegressionSettings
|
|
1036
|
+
}
|
|
1037
|
+
|
|
1024
1038
|
type MatrixPlotsEntry = {
|
|
1025
1039
|
name: string
|
|
1026
1040
|
file: string
|
|
@@ -1132,17 +1146,13 @@ keep this setting here for reason of:
|
|
|
1132
1146
|
matrix?: Matrix
|
|
1133
1147
|
numericDictTermCluster?: NumericDictTermCluster
|
|
1134
1148
|
survival?: Survival
|
|
1149
|
+
regression?: Regression
|
|
1135
1150
|
logscaleBase2?: boolean
|
|
1136
1151
|
plotConfigByCohort?: PlotConfigByCohort
|
|
1137
1152
|
/** Functionality */
|
|
1138
1153
|
dataDownloadCatch?: DataDownloadCatch
|
|
1139
1154
|
helpPages?: URLEntry[]
|
|
1140
1155
|
multipleTestingCorrection?: MultipleTestingCorrection
|
|
1141
|
-
/** regression settings for neuro-oncology portals:
|
|
1142
|
-
- no interaction terms
|
|
1143
|
-
- report event counts of cox coefficients
|
|
1144
|
-
- hide type III stats and miscellaneous statistical tests */
|
|
1145
|
-
neuroOncRegression?: boolean
|
|
1146
1156
|
urlTemplates?: {
|
|
1147
1157
|
/** gene link definition */
|
|
1148
1158
|
gene?: UrlTemplateBase
|
|
@@ -1676,15 +1686,10 @@ export type PreInit = {
|
|
|
1676
1686
|
}
|
|
1677
1687
|
}
|
|
1678
1688
|
|
|
1679
|
-
/**
|
|
1680
|
-
|
|
1681
|
-
- the callback can have arbitrary logic based on requirements from this ds
|
|
1682
|
-
- can supply ()=>false to hide charts that will otherwise shown
|
|
1683
|
-
- can define arbitrary chart type names for purpose-specific charts
|
|
1684
|
-
*/
|
|
1685
|
-
|
|
1689
|
+
/** see details in termdb.server.init.ts
|
|
1690
|
+
*/
|
|
1686
1691
|
export type isSupportedChartCallbacks = {
|
|
1687
|
-
[chartType: string]: (f: any
|
|
1692
|
+
[chartType: string]: (f: any) => boolean | undefined
|
|
1688
1693
|
}
|
|
1689
1694
|
|
|
1690
1695
|
export type Mds3 = BaseMds & {
|
|
@@ -62,11 +62,11 @@ export type BoxPlotData = {
|
|
|
62
62
|
}
|
|
63
63
|
|
|
64
64
|
export type BoxPlotDescrStatsEntry = {
|
|
65
|
-
/** Use lower case for sanity check
|
|
66
|
-
|
|
67
|
-
|
|
68
|
-
id: string
|
|
65
|
+
/** Short hand for summary stat. Use lower case for sanity check */
|
|
66
|
+
id: 'total' | 'min' | 'p25' | 'median' | 'mean' | 'p75' | 'max' | 'sd' | 'variance' | 'iqr' | string
|
|
67
|
+
/** Full label displayed to the user */
|
|
69
68
|
label: string
|
|
69
|
+
/** Calculated value. */
|
|
70
70
|
value: number
|
|
71
71
|
}
|
|
72
72
|
|
|
@@ -89,11 +89,8 @@ export type ViolinPlotEntry = {
|
|
|
89
89
|
seriesId: string
|
|
90
90
|
/** Plot image to display */
|
|
91
91
|
src: string
|
|
92
|
-
|
|
93
|
-
|
|
94
|
-
values: ValuesEntries[]
|
|
95
|
-
}
|
|
96
|
-
uncomputableValueObj: { [index: string]: number } | null
|
|
92
|
+
/** Descriptive stats (i.e. min, max, sd, etc.) */
|
|
93
|
+
summaryStats: ValuesEntries[]
|
|
97
94
|
}
|
|
98
95
|
|
|
99
96
|
export type ViolinResponse = ValidResponse | ErrorResponse
|
|
@@ -105,7 +102,7 @@ type ValidResponse = {
|
|
|
105
102
|
max: number
|
|
106
103
|
plots: ViolinPlotEntry[]
|
|
107
104
|
pvalues?: PValueEntries[][]
|
|
108
|
-
|
|
105
|
+
uncomputableValues: { [index: string]: number }[] | null
|
|
109
106
|
}
|
|
110
107
|
|
|
111
108
|
export const violinPayload: RoutePayload = {
|
package/src/termdb.matrix.ts
CHANGED
|
@@ -6,20 +6,21 @@
|
|
|
6
6
|
* Use this type for that purpose.
|
|
7
7
|
*/
|
|
8
8
|
|
|
9
|
+
type SampleEntry = {
|
|
10
|
+
/** stringified integer sample id */
|
|
11
|
+
sample: string | number
|
|
12
|
+
} & {
|
|
13
|
+
/** key and values for terms, separated by tw.$id */
|
|
14
|
+
[index: string]: {
|
|
15
|
+
key: number
|
|
16
|
+
value: number
|
|
17
|
+
}
|
|
18
|
+
}
|
|
19
|
+
|
|
9
20
|
export type ValidGetDataResponse = {
|
|
10
|
-
samples:
|
|
11
|
-
string
|
|
12
|
-
|
|
13
|
-
/** stringified integer sample id */
|
|
14
|
-
key: number
|
|
15
|
-
/** value: {
|
|
16
|
-
sample: integerId,
|
|
17
|
-
<tw.$id>: {key, value},
|
|
18
|
-
<more terms...>
|
|
19
|
-
} */
|
|
20
|
-
value: number
|
|
21
|
-
}
|
|
22
|
-
>
|
|
21
|
+
samples: {
|
|
22
|
+
[index: string | number]: SampleEntry
|
|
23
|
+
}
|
|
23
24
|
/** Metadata */
|
|
24
25
|
refs: {
|
|
25
26
|
/** metadata about terms
|