@sjcrh/proteinpaint-server 2.39.5 → 2.40.0
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/package.json +1 -1
- package/routes/gdc.maf.ts +3 -2
- package/routes/gdc.topMutatedGenes.ts +360 -132
- package/routes/hicdata.ts +1 -1
- package/routes/termdb.singleSampleMutation.ts +1 -1
- package/routes/termdb.violin.ts +0 -1
- package/server.js +1 -1
- package/server.js.map +1 -1
- package/shared/common.js +6 -0
- package/src/mds3.gdc.filter.js +44 -14
- package/utils/hclust.R +3 -1
package/shared/common.js
CHANGED
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@@ -31,6 +31,7 @@ export const dtdel = 7
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export const dtnloss = 8
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export const dtcloss = 9
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export const dtloh = 10 // to be used in svcnv track
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+
export const plotColor = '#ce768e'
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export const dt2label = {
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[dtsnvindel]: 'SNV/indel',
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@@ -299,6 +300,11 @@ mclass[mclassdeletion] = {
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}
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// TODO complex indel
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export const dt2color = {
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[dtsnvindel]: mclass.M.color // general color for snvindel irrespective of class (when class is not available)
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// add new dt as needed
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}
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+
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// option to override mutation class attribute values
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export function applyOverrides(overrides = {}) {
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if (overrides.mclass) {
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package/src/mds3.gdc.filter.js
CHANGED
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@@ -29,7 +29,9 @@ export function filter2GDCfilter(f) {
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}
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}
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obj.content.push(f)
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-
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continue
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}
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if (item.tvs.ranges) {
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for (const range of item.tvs.ranges) {
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if (range.startunbounded) {
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obj.content.push({
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@@ -45,21 +47,49 @@ export function filter2GDCfilter(f) {
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})
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continue
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}
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-
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-
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-
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-
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-
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-
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if (item.tvs.isnot) {
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obj.content.push({
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op: 'or',
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content: [
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{
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op: 'and',
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content: [
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{
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op: range.startinclusive ? '<' : '<=',
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content: { field: mayChangeCase2Cases(item.tvs.term.id), value: range.start }
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}
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]
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},
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{
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op: 'and',
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content: [
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{
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op: range.stopinclusive ? '>' : '>=',
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content: { field: mayChangeCase2Cases(item.tvs.term.id), value: range.stop }
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}
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]
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}
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]
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})
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} else {
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obj.content.push({
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op: 'and',
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content: [
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{
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op: range.startinclusive ? '>=' : '>',
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content: { field: mayChangeCase2Cases(item.tvs.term.id), value: range.start }
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},
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{
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op: range.stopinclusive ? '<=' : '<',
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content: { field: mayChangeCase2Cases(item.tvs.term.id), value: range.stop }
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}
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]
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})
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}
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}
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continue
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}
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throw 'unknown tvs structure when converting to gdc filter'
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}
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return obj
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}
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package/utils/hclust.R
CHANGED
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@@ -14,7 +14,9 @@
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# To plot the heatmap uncomment line `library(ggplot2) and lines after "Visualization" comment
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-
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suppressWarnings({
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suppressPackageStartupMessages(library(jsonlite))
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})
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#library(flashClust)
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#library(ggplot2) # Uncomment this line to plot heatmap in R
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