@sjcrh/proteinpaint-types 2.98.0 → 2.98.1

package/dist/{chunk-WCMW6A75.js → chunk-Y4KYTIK6.js}

@@ -24,7 +24,7 @@ var validTermdbTopVariablyExpressedGenesRequest = (input) => {
     const $join = import_typia.createValidate.join;
     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;
     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));
-    const $io2 = (input3) => "var" === input3.type || "iqr" === input3.type;
+    const $io2 = (input3) => "iqr" === input3.type || "var" === input3.type;
     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)));
     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)));
     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));
@@ -221,7 +221,7 @@ var validTermdbTopVariablyExpressedGenesRequest = (input) => {
         expected: "(Array<string> | null)",
         value: input3.geneList
       })].every((flag) => flag);
-      const $vo2 = (input3, _path2, _exceptionable2 = true) => ["var" === input3.type || "iqr" === input3.type || $report(_exceptionable2, {
+      const $vo2 = (input3, _path2, _exceptionable2 = true) => ["iqr" === input3.type || "var" === input3.type || $report(_exceptionable2, {
         path: _path2 + ".type",
         expected: '("iqr" | "var")',
         value: input3.type

package/dist/correlationVolcano.js

@@ -0,0 +1,11 @@
+import {
+  CorrelationVolcanoPayload,
+  validCorrelationVolcanoRequest,
+  validCorrelationVolcanoResponse
+} from "./chunk-DFSJACIQ.js";
+import "./chunk-Z6B6IQIY.js";
+export {
+  CorrelationVolcanoPayload,
+  validCorrelationVolcanoRequest,
+  validCorrelationVolcanoResponse
+};

package/dist/index.js

@@ -1,13 +1,18 @@
+import {
+  termdbTopTermsByTypePayload,
+  validTermdbTopTermsByTypeRequest,
+  validTermdbTopTermsByTypeResponse
+} from "./chunk-CU5TLT6P.js";
 import {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,
   validTermdbTopVariablyExpressedGenesResponse
-} from "./chunk-WCMW6A75.js";
+} from "./chunk-Y4KYTIK6.js";
 import {
   validViolinRequest,
   validViolinResponse,
   violinPayload
-} from "./chunk-SRDMLS6D.js";
+} from "./chunk-GQVW2DPA.js";
 import {
   tilePayload,
   validTileRequest,
@@ -18,6 +23,11 @@ import {
   validWSImagesResponse,
   wsImagesPayload
 } from "./chunk-XLBSZOMF.js";
+import {
+  rootTermPayload,
+  validRootTermRequest,
+  validRootTermResponse
+} from "./chunk-GU7LIGHN.js";
 import {
   termdbSampleImagesPayload,
   validTermdbSampleImagesRequest,
@@ -54,10 +64,10 @@ import {
   validTermsByIdsResponse
 } from "./chunk-7K726NBK.js";
 import {
-  termdbTopTermsByTypePayload,
-  validTermdbTopTermsByTypeRequest,
-  validTermdbTopTermsByTypeResponse
-} from "./chunk-CU5TLT6P.js";
+  boxplotPayload,
+  validBoxPlotRequest,
+  validBoxPlotResponse
+} from "./chunk-X36QKCNU.js";
 import {
   termdbCategoriesPayload,
   validCategoriesRequest,
@@ -94,10 +104,10 @@ import {
   validPercentileResponse
 } from "./chunk-IORCECK2.js";
 import {
-  rootTermPayload,
-  validRootTermRequest,
-  validRootTermResponse
-} from "./chunk-GU7LIGHN.js";
+  hicstatPayload,
+  validHicstatRequest,
+  validHicstatResponse
+} from "./chunk-QX7QLUKY.js";
 import {
   isoformlstPayload,
   validIsoformLstRequest,
@@ -129,10 +139,10 @@ import {
   validDEResponse
 } from "./chunk-Z2WFGV6V.js";
 import {
-  boxplotPayload,
-  validBoxPlotRequest,
-  validBoxPlotResponse
-} from "./chunk-OAO3UWUX.js";
+  GdcMafPayload,
+  validGdcMafBuildRequest,
+  validGdcMafBuildResponse
+} from "./chunk-DIDZMC3G.js";
 import {
   gdcTopMutatedGenePayload,
   validGdcTopMutatedGeneRequest,
@@ -168,11 +178,6 @@ import {
   validHicGenomeRequest,
   validHicGenomeResponse
 } from "./chunk-W3QYIXXF.js";
-import {
-  hicstatPayload,
-  validHicstatRequest,
-  validHicstatResponse
-} from "./chunk-QX7QLUKY.js";
 import {
   brainImagingPayload,
   validBrainImagingRequest,
@@ -188,6 +193,11 @@ import {
   validBurdenRequest,
   validBurdenResponse
 } from "./chunk-RLFGMVJZ.js";
+import {
+  CorrelationVolcanoPayload,
+  validCorrelationVolcanoRequest,
+  validCorrelationVolcanoResponse
+} from "./chunk-DFSJACIQ.js";
 import {
   datasetPayload,
   validDatasetRequest,
@@ -208,13 +218,9 @@ import {
   validGdcMafRequest,
   validGdcMafResponse
 } from "./chunk-CETMA2FU.js";
-import {
-  GdcMafPayload,
-  validGdcMafBuildRequest,
-  validGdcMafBuildResponse
-} from "./chunk-DIDZMC3G.js";
 import "./chunk-Z6B6IQIY.js";
 export {
+  CorrelationVolcanoPayload,
   GdcMafPayload,
   boxplotPayload,
   brainImagingPayload,
@@ -266,6 +272,8 @@ export {
   validBurdenResponse,
   validCategoriesRequest,
   validCategoriesResponse,
+  validCorrelationVolcanoRequest,
+  validCorrelationVolcanoResponse,
   validDERequest,
   validDEResponse,
   validDZImagesRequest,

package/dist/termdb.boxplot.js

@@ -2,7 +2,7 @@ import {
   boxplotPayload,
   validBoxPlotRequest,
   validBoxPlotResponse
-} from "./chunk-OAO3UWUX.js";
+} from "./chunk-X36QKCNU.js";
 import "./chunk-Z6B6IQIY.js";
 export {
   boxplotPayload,

package/dist/termdb.topVariablyExpressedGenes.js

@@ -2,7 +2,7 @@ import {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,
   validTermdbTopVariablyExpressedGenesResponse
-} from "./chunk-WCMW6A75.js";
+} from "./chunk-Y4KYTIK6.js";
 import "./chunk-Z6B6IQIY.js";
 export {
   termdbTopVariablyExpressedGenesPayload,

package/dist/termdb.violin.js

@@ -2,7 +2,7 @@ import {
   validViolinRequest,
   validViolinResponse,
   violinPayload
-} from "./chunk-SRDMLS6D.js";
+} from "./chunk-GQVW2DPA.js";
 import "./chunk-Z6B6IQIY.js";
 export {
   validViolinRequest,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.98.0",
+  "version": "2.98.1",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -838,15 +838,18 @@ type SelectCohortValuesEntry = {
 }
 
 export type SelectCohortEntry = {
+	/** subcohort term in db. uses hardcoded type=multivalue */
 	term: { id: string; type: string }
 	/** Title above the cohort introduction/content in the about tab */
 	title?: string
 	/** Text above radio cohort options in the about tab. */
 	prompt: string
 	values: SelectCohortValuesEntry[]
+	/** cohort-related static html shown in about tab */
 	description?: string
-	/* If the description is dependent on the user pass a descriptionByUser dict instead */
-	descriptionByUser?: { [index: string]: string }
+	/** If the description is dependent on the user's role, 
+	define this callback to return description based on auth */
+	descriptionByUser?: (auth: any) => string
 	/** subtext shown at the very bottom of the cohort/about tab subheader */
 	asterisk?: string
 	//The profile has clearOnChange. The terms used in the plots are not always the same for the profile.
@@ -895,6 +898,22 @@ this is limited to only one term and doesn't allow switching between multiple te
 type Scatterplots = {
 	plots: ScatterPlotsEntry[]
 }
+/** this plot compares correlation of one feature against a bunch of variables across samples
+ */
+type CorrelationVolcano = {
+	/** fixed feature, is one numeric term */
+	feature: {
+		/** later expand to other types */
+		termType: 'geneExpression'
+	}
+	/** list of numeric variables to be compared against fixed feature*/
+	variables: {
+		/** later can expand */
+		type: 'dictionaryTerm'
+		/** when type=dictionaryTerm, is array of numeric term ids */
+		termIds?: string[]
+	}
+}
 
 type MatrixSettingsControlLabels = {
 	samples?: string
@@ -951,6 +970,15 @@ type SurvivalSettings = {
 	xTickValues?: number[]
 }
 
+type RegressionSettings = {
+	/** disable interactions */
+	disableInteractions?: boolean
+	/** hide type III statistics table in results */
+	hideType3?: boolean
+	/** hide statistical tests table in results */
+	hideTests?: boolean
+}
+
 type MatrixSettings = {
 	maxSample?: number
 	svgCanvasSwitch?: number
@@ -1021,6 +1049,11 @@ type Survival = {
 	settings?: SurvivalSettings
 }
 
+type Regression = {
+	/** default settings for regression */
+	settings?: RegressionSettings
+}
+
 type MatrixPlotsEntry = {
 	name: string
 	file: string
@@ -1128,21 +1161,16 @@ keep this setting here for reason of:
   */
 	useLower?: boolean
 
-	scatterplots?: Scatterplots
 	matrix?: Matrix
 	numericDictTermCluster?: NumericDictTermCluster
 	survival?: Survival
+	regression?: Regression
 	logscaleBase2?: boolean
 	plotConfigByCohort?: PlotConfigByCohort
 	/** Functionality */
 	dataDownloadCatch?: DataDownloadCatch
 	helpPages?: URLEntry[]
 	multipleTestingCorrection?: MultipleTestingCorrection
-	/** regression settings for neuro-oncology portals:
-- no interaction terms
-- report event counts of cox coefficients
-- hide type III stats and miscellaneous statistical tests */
-	neuroOncRegression?: boolean
 	urlTemplates?: {
 		/** gene link definition */
 		gene?: UrlTemplateBase
@@ -1270,6 +1298,8 @@ type AssayAvailability = {
 
 //Shared with genome.ts
 export type Cohort = {
+	/** if present, means correlation volcano plot analysis is enabled */
+	correlationVolcano?: CorrelationVolcano
 	cumburden?: {
 		files: {
 			fit: string
@@ -1285,6 +1315,7 @@ export type Cohort = {
 	matrixplots?: MatrixPlots
 	mutationset?: MutationSet[]
 	renamedChartTypes?: { singleCellPlot?: string; sampleScatter?: string }
+	/** if present, supplies premade scatter plots */
 	scatterplots?: Scatterplots
 	termdb: Termdb
 }
@@ -1676,15 +1707,10 @@ export type PreInit = {
 	}
 }
 
-/** supply "isSupported()" kind of callback per chart type,
-	that will overwrite default logic in getSupportedChartTypes()
-	- the callback can have arbitrary logic based on requirements from this ds
-	- can supply ()=>false to hide charts that will otherwise shown
-	- can define arbitrary chart type names for purpose-specific charts
-*/
-
+/** see details in termdb.server.init.ts
+ */
 export type isSupportedChartCallbacks = {
-	[chartType: string]: (f: any, auth: any) => boolean | undefined
+	[chartType: string]: (f: any) => boolean | undefined
 }
 
 export type Mds3 = BaseMds & {

package/src/index.ts

@@ -8,6 +8,7 @@ export * from './routes/routeApi.ts'
 export * from './routes/brainImaging.ts'
 export * from './routes/brainImagingSamples.ts'
 export * from './routes/burden.ts'
+export * from './routes/correlationVolcano.ts'
 export * from './routes/dataset.ts'
 export * from './routes/dsdata.ts'
 export * from './routes/dzimages.ts'

package/src/routes/correlationVolcano.ts

@@ -0,0 +1,44 @@
+import type { RoutePayload } from './routeApi.js'
+import type { TermWrapper } from '../terms/tw.ts'
+import type { Filter } from '../filter.ts'
+
+/** */
+export type CorrelationVolcanoRequest = {
+	genome: string
+	dslabel: string
+	filter?: Filter
+	filter0?: any // gdc
+	/** feature tw */
+	featureTw: TermWrapper
+	/** variables */
+	variableTwLst: TermWrapper[]
+	/** correlation method */
+	correlationMethod: 'pearson' | 'spearman'
+	/** add new param */
+}
+
+export type CorrelationVolcanoResponse = {
+	/** each element is test result of one variable corresponding to variableTwLst */
+	variableItems: {
+		/** correlation coefficient, -1 to 1 */
+		correlation: number
+		/** pvalue */
+		original_pvalue: number
+		/** pvalue */
+		adjusted_pvalue: number
+		/** tw.$id, for client to match the item with variableTwLst */
+		tw$id: string
+		/** number of samples analyzed. samples not having complete data for all terms will be excluded, thus size may be lower than current cohort */
+		sampleSize: number
+	}[]
+}
+
+export const CorrelationVolcanoPayload: RoutePayload = {
+	request: {
+		typeId: 'CorrelationVolcanoRequest'
+	},
+	response: {
+		typeId: 'CorrelationVolcanoResponse'
+	}
+	//examples: []
+}

package/src/routes/termdb.boxplot.ts

@@ -1,18 +1,20 @@
 import type { RoutePayload } from './routeApi.js'
+import type { TermWrapper } from '../terms/tw.ts'
+import type { Filter } from '../filter.ts'
 
 /**Args set in Termdb vocab and from mass box plot */
 export type BoxPlotRequest = {
 	/** Args set in TermVocab */
 	/** term1 or term */
-	tw: any
+	tw: TermWrapper
 	genome: string
 	dslabel: string
 	/** sort plots by median value */
 	orderByMedian: boolean
 	/** term2 */
-	overlayTw?: any
-	filter: any
-	filter0: any
+	overlayTw?: TermWrapper
+	filter?: Filter
+	filter0?: any
 }
 
 export type BoxPlotResponse = {
@@ -62,11 +64,11 @@ export type BoxPlotData = {
 }
 
 export type BoxPlotDescrStatsEntry = {
-	/** Use lower case for sanity check
-	 * 'total' | 'min' | 'p25' | 'median' | 'mean' | 'p75' | 'max' | 'sd' | 'variance' | 'iqr'
-	 */
-	id: string
+	/** Short hand for summary stat. Use lower case for sanity check */
+	id: 'total' | 'min' | 'p25' | 'median' | 'mean' | 'p75' | 'max' | 'sd' | 'variance' | 'iqr' | string
+	/** Full label displayed to the user */
 	label: string
+	/** Calculated value. */
 	value: number
 }
 

package/src/routes/termdb.violin.ts

@@ -89,11 +89,8 @@ export type ViolinPlotEntry = {
 	seriesId: string
 	/** Plot image to display */
 	src: string
-	summaryStats: {
-		/** Descriptive stats (i.e. min, max, sd, etc.) */
-		values: ValuesEntries[]
-	}
-	uncomputableValueObj: { [index: string]: number } | null
+	/** Descriptive stats (i.e. min, max, sd, etc.) */
+	summaryStats: ValuesEntries[]
 }
 
 export type ViolinResponse = ValidResponse | ErrorResponse
@@ -105,7 +102,7 @@ type ValidResponse = {
 	max: number
 	plots: ViolinPlotEntry[]
 	pvalues?: PValueEntries[][]
-	uncomputableValueObj: { [index: string]: number }[] | null
+	uncomputableValues: { [index: string]: number }[] | null
 }
 
 export const violinPayload: RoutePayload = {

package/src/termdb.matrix.ts

@@ -6,20 +6,21 @@
  * Use this type for that purpose.
  */
 
+type SampleEntry = {
+	/** stringified integer sample id  */
+	sample: string | number
+} & {
+	/** key and values for terms, separated by tw.$id */
+	[index: string]: {
+		key: number
+		value: number
+	}
+}
+
 export type ValidGetDataResponse = {
-	samples: Record<
-		string,
-		{
-			/** stringified integer sample id  */
-			key: number
-			/** value: { 
-			sample: integerId,
-			<tw.$id>: {key, value},
-			<more terms...>
-		} */
-			value: number
-		}
-	>
+	samples: {
+		[index: string | number]: SampleEntry
+	}
 	/** Metadata */
 	refs: {
 		/** metadata about terms