@sjcrh/proteinpaint-types 2.180.1 → 2.182.0

package/dist/termdb.chat2.js

@@ -1,7 +1,7 @@
 import {
   validChatRequest,
   validChatResponse
-} from "./chunk-ICACMXK2.js";
+} from "./chunk-ZKO7LMCC.js";
 import {
   ChatPayload
 } from "./chunk-FRXRNCDV.js";

package/dist/termdb.cluster.js

@@ -2,7 +2,7 @@ import {
   termdbClusterPayload,
   validTermdbClusterRequest,
   validTermdbClusterResponse
-} from "./chunk-6PTYP7X4.js";
+} from "./chunk-UYKWZWCU.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbClusterPayload,

package/dist/termdb.descrstats.js

@@ -2,7 +2,7 @@ import {
   descrStatsPayload,
   validDescrStatsRequest,
   validDescrStatsResponse
-} from "./chunk-Y6F7ZVSV.js";
+} from "./chunk-45VA4Y6L.js";
 import "./chunk-YNHC5SXO.js";
 export {
   descrStatsPayload,

package/dist/termdb.diffMeth.js

@@ -2,7 +2,7 @@ import {
   diffMethPayload,
   validDiffMethRequest,
   validDiffMethResponse
-} from "./chunk-4DCPDZW4.js";
+} from "./chunk-G6ZTAMGK.js";
 import "./chunk-YNHC5SXO.js";
 export {
   diffMethPayload,

package/dist/termdb.dmr.js

@@ -2,7 +2,7 @@ import {
   TermdbDmrPayload,
   validTermdbDmrRequest,
   validTermdbDmrResponse
-} from "./chunk-P75GBHFO.js";
+} from "./chunk-K6W2WEPW.js";
 import "./chunk-YNHC5SXO.js";
 export {
   TermdbDmrPayload,

package/dist/termdb.isoformAvailability.js

@@ -0,0 +1,11 @@
+import {
+  TermdbIsoformAvailabilityPayload,
+  validTermdbIsoformAvailabilityRequest,
+  validTermdbIsoformAvailabilityResponse
+} from "./chunk-7OA6G77M.js";
+import "./chunk-YNHC5SXO.js";
+export {
+  TermdbIsoformAvailabilityPayload,
+  validTermdbIsoformAvailabilityRequest,
+  validTermdbIsoformAvailabilityResponse
+};

package/dist/termdb.numericcategories.js

@@ -2,7 +2,7 @@ import {
   numericCategoriesPayload,
   validNumericCategoriesRequest,
   validNumericCategoriesResponse
-} from "./chunk-PZUKZRSI.js";
+} from "./chunk-DDMUMMOL.js";
 import "./chunk-YNHC5SXO.js";
 export {
   numericCategoriesPayload,

package/dist/termdb.percentile.js

@@ -2,7 +2,7 @@ import {
   percentilePayload,
   validPercentileRequest,
   validPercentileResponse
-} from "./chunk-KFNXZOED.js";
+} from "./chunk-ZRTB7SRA.js";
 import "./chunk-YNHC5SXO.js";
 export {
   percentilePayload,

package/dist/termdb.termsbyids.js

@@ -2,7 +2,7 @@ import {
   termsByIdsPayload,
   validTermsByIdsRequest,
   validTermsByIdsResponse
-} from "./chunk-DIKDKRFN.js";
+} from "./chunk-3DA4MJ2U.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termsByIdsPayload,

package/dist/termdb.topTermsByType.js

@@ -2,7 +2,7 @@ import {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,
   validTermdbTopTermsByTypeResponse
-} from "./chunk-XCSFBW4V.js";
+} from "./chunk-2QTCQFYE.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbTopTermsByTypePayload,

package/dist/termdb.topVariablyExpressedGenes.js

@@ -2,7 +2,7 @@ import {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,
   validTermdbTopVariablyExpressedGenesResponse
-} from "./chunk-OT6W3FNI.js";
+} from "./chunk-VUNM6QTX.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbTopVariablyExpressedGenesPayload,

package/dist/termdb.violinBox.js

@@ -0,0 +1,11 @@
+import {
+  validViolinBoxRequest,
+  validViolinBoxResponse,
+  violinBoxPayload
+} from "./chunk-C5ECCXOT.js";
+import "./chunk-YNHC5SXO.js";
+export {
+  validViolinBoxRequest,
+  validViolinBoxResponse,
+  violinBoxPayload
+};

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.180.1",
+  "version": "2.182.0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -72,9 +72,9 @@ type InfoFieldEntry = {
 
 /*
 type GenomicPositionEntry = {
-                chr: string
-                start: number
-                stop: number
+	chr: string
+	start: number
+	stop: number
 }
 */
 
@@ -175,12 +175,12 @@ type DictApi = {
 type SnvIndelFormat = {
 	[index: string]: {
 		/* has value for a non-GT field indicating the variant 
-        is annotated to this sample*/
+		is annotated to this sample*/
 		ID: string
 		Description: string
 		/** 'R' or 1. do not parse values here based on Number="R"
-        as we don't need to compute on the format values on backend
-        client will parse the values for display */
+		as we don't need to compute on the format values on backend
+		client will parse the values for display */
 		Number: string | number
 		Type: string
 	}
@@ -292,15 +292,15 @@ type SnvindelComputeDetails = {
 		name: string
 	}[]
 	/** a type of computing decides numeric values for each variant displayed in tk
-    computing type is also determined by number of groups
-    if only 1 group:
-         type=info: use numeric info field
-         type=filter: use AF
-         type=population: use AF
-    if there're two groups:
-         both types are "filter": allow AF diff or fisher
-         "filter" and "population": allow AF diff or fisher
-         else: value difference
+	computing type is also determined by number of groups
+	if only 1 group:
+		 type=info: use numeric info field
+		 type=filter: use AF
+		 type=population: use AF
+	if there're two groups:
+		 both types are "filter": allow AF diff or fisher
+		 "filter" and "population": allow AF diff or fisher
+		 else: value difference
 	*/
 	groups: (SnvindelComputeGroup_filter | SnvindelComputeGroup_population | SnvindelComputeGroup_info)[]
 	/** define lists of group-comparison methods to compute one numerical value per variant
@@ -520,11 +520,11 @@ type TrackLst = {
 
 	[
 	  {
-         "isfacet": true,
-         "name": "PEDDEP Prepilot",
-         "tracks": [
+		 "isfacet": true,
+		 "name": "PEDDEP Prepilot",
+		 "tracks": [
 		   {
-		     name:str // required. used as *identifer* for a track
+			 name:str // required. used as *identifer* for a track
 			 sample:str // required. should match with a sample in db!
 			 assay:str // required. free string not controlled in dictionary yet. if missing the track won't appear in facet table
 			 type:str // properties inherent for each custom track
@@ -681,7 +681,7 @@ for a given region, the median signal from probes in the region is used to make
 this is alternative to CnvSegmentQuery
 
 type Probe2Cnv = {
-                file: string
+	file: string
 }
 */
 
@@ -711,6 +711,7 @@ export type MetaboliteIntensityQuery = MetaboliteIntensityQueryNative
 type CohortConfig = {
 	file: string
 	filter?: Tvs[]
+	overlayTerm?: BaseTerm
 }
 type AssayWithCohorts = {
 	cohorts: {
@@ -757,6 +758,24 @@ export type GeneExpressionQuery = {
 	unit?: string
 }
 
+/** Isoform expression query — either .get() or .file is needed.
+ *  availableItems is populated at startup from the HDF5 item dataset
+ *  so the client can filter isoform selection lists. */
+export type IsoformExpressionQuery = {
+	/** ds-supplied or dynamically added getter */
+	get?: (param: any, ds: any) => void
+	/** HDF5 file with ENST IDs as row keys */
+	file?: string
+	/** dynamically added during server launch, list of sample integer IDs from file */
+	samples?: number[]
+	/** cache for default bins per isoform */
+	geneExpression2bins?: { [index: string]: any }
+	/** expression unit (e.g. 'TPM') */
+	unit?: string
+	/** ENST IDs available in the HDF5 file, populated during server validation */
+	availableItems?: string[]
+}
+
 export type SingleCellGeneExpressionNative = {
 	src: 'native'
 	/** path to HDF5 files. for now only HDF5 is supported.
@@ -999,6 +1018,7 @@ type Mds3Queries = {
 	singleSampleMutation?: SingleSampleMutationQuery
 	NIdata?: NIdataQuery
 	geneExpression?: GeneExpressionQuery
+	isoformExpression?: IsoformExpressionQuery
 	/** single-sample gsea precomputed scores for rnaseq samples, for genesets from geneset db
 	requires genome to be equipped with geneset db
 	*/
@@ -1418,13 +1438,19 @@ type UrlTemplateBase = {
 }
 export type UrlTemplateSsm = UrlTemplateBase & {
 	/** to create separate link, but not directly on chr.pos.ref.alt string.
-    name of link is determined by either namekey or linkText. former allows to retrieve a name per m that's different from chr.pos.xx */
+	name of link is determined by either namekey or linkText. former allows to retrieve a name per m that's different from chr.pos.xx */
 	shownSeparately?: boolean
 	/** optional name of link, if set, same name will be used for all links. e.g. "ClinVar".
 if missing, name is value of m[url.namekey], as used in url itself (e.g. snp rsid) */
 	linkText?: string
 }
 
+export type GetSamplesOpts = {
+	filter: any // pp filter
+	filter0: any // mmrf filter
+	ds: any
+}
+
 /*** type of ds.cohort.termdb{} ***/
 export type Termdb = {
 	/** Terms */
@@ -1457,7 +1483,7 @@ export type Termdb = {
 	/** if true, backend is allowed to send sample names to client in charts */
 	displaySampleIds?: (clientAuthResult: any) => boolean
 	/** get samples that match supplied filter */
-	getSamples?: (filter: any, ds: any) => Promise<Set<any>>
+	getSamples?: (opts: GetSamplesOpts) => Promise<Set<any>>
 	converSampleIds?: boolean
 	alwaysShowBranchTerms?: boolean
 	minimumSampleAllowed4filter?: number
@@ -1567,9 +1593,9 @@ keep this setting here for reason of:
 	hierCluster?: any
 
 	/** ds customization of rules in TermTypeSelect on what term type to exclude for a usecase.
-    used by gdc in that gene exp cannot be used for filtering
-    note this applies to left-side term type tabs, but not terms in dict tree. latter is controlled by excludeTermtypeByTarget
-    */
+	used by gdc in that gene exp cannot be used for filtering
+	note this applies to left-side term type tabs, but not terms in dict tree. latter is controlled by excludeTermtypeByTarget
+	*/
 	useCasesExcluded?: {
 		/** key is target name (todo restrict values), value is array of 1 or more term
 		 * types (todo restrict values) */
@@ -1819,39 +1845,12 @@ type MassNav = {
 	tabs?: {
 		/** supported keys: about, charts, groups, filter
 		invalid key is ignored
-		when dslabel is too long to show in about tab middl row or to define alternative label, do .tabs:{about:{mid:'alt label'}}
-		*/
-		[index: string]: {
-			/** show in a specific order of tabs */
-			order?: number
-			/** label appearing in the top row in upper case */
-			top?: string
-			/** biggest label appearing in the middle row */
-			mid?: string
-			/** label appearing in the bottom row*/
-			btm?: string
-			/** if true, does not show the tab */
-			hide?: boolean
-			/** static html contents to show specifically in "about" tab subheader
-			 * maybe used for other tabs as well.
-			 */
-			html?: string
-			/** declare data release. should only use for "about" */
-			dataRelease?: {
-				/** data release version */
-				version: string
-				/** link to data release page */
-				link: string
-			}
-			/** html string, can include links to other
-			 * pages (e.g., tutorials, google group) */
-			additionalInfo?: string
-			/** "active" items, shown as clickable buttons in about tab. click an item to launch a plot */
-			activeItems?: {
-				items: ActiveItem[]
-				// can add holderStyle to customize
-			}
-		}
+		when dslabel is too long to show in about tab middle row or to define alternative label, 
+		do .tabs:{about:{mid:'alt label'}} */
+		about?: MassNavAboutTabEntry
+		charts?: MassNavTabEntry
+		groups?: MassNavTabEntry
+		filter?: MassNavTabEntry
 	}
 	/** customize background color of active navigation tab */
 	activeColor?: string
@@ -1859,6 +1858,41 @@ type MassNav = {
 	activeColorHover?: string
 }
 
+type MassNavTabEntry = {
+	/** show in a specific order of tabs */
+	order?: number
+	/** label appearing in the top row in upper case */
+	top?: string
+	/** biggest label appearing in the middle row */
+	mid?: string
+	/** label appearing in the bottom row*/
+	btm?: string
+	/** if true, does not show the tab */
+	hide?: boolean
+}
+
+type MassNavAboutTabEntry = MassNavTabEntry & {
+	/** html string, can include links to other
+	 * pages (e.g., tutorials, google group) */
+	additionalInfo?: string
+	/** static html contents to show specifically in "about" tab subheader
+	 * maybe used for other tabs as well.
+	 * Will not render if cohort.termdb.selectCohort is present */
+	html?: string
+	/** declare data release. Shown with the server info */
+	dataRelease?: {
+		/** data release version */
+		version: string
+		/** link to data release page */
+		link: string
+	}
+	/** "active" items, shown as clickable buttons in about tab. click an item to launch a plot */
+	activeItems?: {
+		items: ActiveItem[]
+		// can add holderStyle to customize
+	}
+}
+
 type ActiveItem = {
 	/** string or html to show inside the button for the item, potentially allow to include <image> as logo */
 	title: string

package/src/index.ts

@@ -38,7 +38,6 @@ export * from './routes/routeApi.ts'
 export * from './routes/samplewsimages.ts'
 export * from './routes/saveWSIAnnotation.ts'
 export * from './routes/snp.ts'
-export * from './routes/termdb.boxplot.ts'
 export * from './routes/termdb.categories.ts'
 export * from './routes/termdb.chat2.ts'
 export * from './routes/termdb.cluster.ts'
@@ -48,6 +47,7 @@ export * from './routes/termdb.DE.ts'
 export * from './routes/termdb.diffMeth.ts'
 export * from './routes/termdb.descrstats.ts'
 export * from './routes/termdb.dmr.ts'
+export * from './routes/termdb.isoformAvailability.ts'
 export * from './routes/termdb.numericcategories.ts'
 export * from './routes/termdb.percentile.ts'
 export * from './routes/termdb.runChart.ts'
@@ -64,7 +64,7 @@ export * from './routes/termdb.termchildren.ts'
 export * from './routes/termdb.topMutatedGenes.ts'
 export * from './routes/termdb.topTermsByType.ts'
 export * from './routes/termdb.topVariablyExpressedGenes.ts'
-export * from './routes/termdb.violin.ts'
+export * from './routes/termdb.violinBox.ts'
 export * from './routes/tileserver.ts'
 export * from './routes/wsimages.ts'
 export * from './routes/wsisamples.ts'
@@ -74,6 +74,7 @@ export * from './terms/date.ts'
 export * from './terms/numeric.ts'
 export * from './terms/geneVariant.ts'
 export * from './terms/geneExpression.ts'
+export * from './terms/isoformExpression.ts'
 export * from './terms/metaboliteIntensity.ts'
 export * from './terms/proteomeAbundance.ts'
 export * from './terms/qualitative.ts'

package/src/routes/termdb.cluster.ts

@@ -3,6 +3,7 @@ import type { ErrorResponse } from './errorResponse.ts'
 import type { Filter } from '../filter.ts'
 import type { Term } from '../terms/term.ts'
 import type { GeneExpressionTW } from '../terms/geneExpression.ts'
+import type { IsoformExpressionTW } from '../terms/isoformExpression.ts'
 import type { MetaboliteIntensityTW } from '../terms/metaboliteIntensity.ts'
 import type { ProteomeAbundanceTW, ProteomeDetails } from '../terms/proteomeAbundance.ts'
 
@@ -48,6 +49,15 @@ export type TermdbClusterRequestMetabolite = TermdbClusterRequestBase & {
 	zScoreTransformation?: string
 }
 
+export type TermdbClusterRequestIsoformExpression = TermdbClusterRequestBase & {
+	/** Data type */
+	dataType: 'isoformExpression'
+	/** List of terms */
+	terms: IsoformExpressionTW[]
+	/** perform z-score transformation on values */
+	zScoreTransformation?: string
+}
+
 export type TermdbClusterRequestProteomeAbundance = TermdbClusterRequestBase & {
 	/** Data type */
 	dataType: 'proteomeAbundance'
@@ -61,6 +71,7 @@ export type TermdbClusterRequestProteomeAbundance = TermdbClusterRequestBase & {
 
 export type TermdbClusterRequest =
 	| TermdbClusterRequestGeneExpression
+	| TermdbClusterRequestIsoformExpression
 	| TermdbClusterRequestMetabolite
 	| TermdbClusterRequestProteomeAbundance
 

package/src/routes/termdb.diffMeth.ts

@@ -31,6 +31,12 @@ export type DiffMethDataEntry = {
 	promoter_id: string
 	/** Gene symbol(s) associated with the promoter (comma-separated if multiple) */
 	gene_name: string
+	/** Chromosome (e.g. "chr1") */
+	chr: string
+	/** Promoter start coordinate (0-based) */
+	start: number
+	/** Promoter end coordinate (exclusive) */
+	stop: number
 	/** M-value difference (positive = hypermethylated in cases) */
 	fold_change: number
 	/** Raw p-value from moderated t-test */

package/src/routes/termdb.dmr.ts

@@ -11,10 +11,26 @@ export type TermdbDmrRequest = {
 	chr: string
 	start: number
 	stop: number
-	/** optional regulatory domain annotations for the GP model */
-	annotations?: DmrAnnotation[]
-	/** max fraction of NaN per probe before dropping (default 0.5) */
-	nan_threshold?: number
+	/** DMRCate lambda parameter: Gaussian kernel bandwidth in nucleotides (default 1000) */
+	lambda?: number
+	/** DMRCate C parameter: scaling factor for kernel width (default 2) */
+	C?: number
+	/** FDR cutoff for CpG significance (default 0.05) */
+	fdr_cutoff?: number
+	/** display name for group1 (e.g. from volcano plot) */
+	group1Name?: string
+	/** display name for group2 (e.g. from volcano plot) */
+	group2Name?: string
+	/** Block width in CSS pixels for server-side track rendering (default 800) */
+	blockWidth?: number
+	/** Device pixel ratio for server-side track rendering (default 1) */
+	devicePixelRatio?: number
+	/** Maximum region size (bp) to show LOESS curves (default 50000) */
+	maxLoessRegion?: number
+	/** Group/DMR colors for server-side track rendering */
+	colors?: { group1: string; group2: string; hyper: string; hypo: string }
+	/** Backend engine: 'rust' (genome-wide eBayes, default) or 'r' (DMRCate via cached limma) */
+	backend?: 'rust' | 'r'
 	filter?: Filter
 	__protected__?: any
 }
@@ -24,12 +40,44 @@ type Sample = {
 	sample: string
 }
 
-type DmrAnnotation = {
-	name: string
-	start: number
-	end: number
-	base_methylation?: number
-	length_scale_bp?: number
+export type DmrLoessCurves = {
+	/** Evenly spaced genomic positions where LOESS was evaluated */
+	positions: number[]
+	/** LOESS fitted values for group 1 (control) */
+	group1_fitted: number[]
+	/** Lower 95% CI bound for group 1 */
+	group1_ci_lower: number[]
+	/** Upper 95% CI bound for group 1 */
+	group1_ci_upper: number[]
+	/** LOESS fitted values for group 2 (case) */
+	group2_fitted: number[]
+	/** Lower 95% CI bound for group 2 */
+	group2_ci_lower: number[]
+	/** Upper 95% CI bound for group 2 */
+	group2_ci_upper: number[]
+}
+
+export type DmrDiagnostic = {
+	probes: {
+		positions: number[]
+		mean_group1: (number | null)[]
+		mean_group2: (number | null)[]
+		fdr: number[]
+		logFC: (number | null)[]
+	}
+	probe_spacings: number[]
+	/** LOESS smoothed curves with 95% CI for both groups */
+	loess?: DmrLoessCurves
+	/** Total probes analyzed genome-wide for eBayes */
+	total_probes_analyzed?: number
+	/** Peak RSS memory in MB */
+	peak_memory_mb?: number
+	/** Starting RSS memory in MB */
+	start_memory_mb?: number
+	/** Total elapsed time in milliseconds */
+	elapsed_ms?: number
+	/** Server-rendered track PNG as data URI (Rust backend only) */
+	track_png?: string | null
 }
 
 export type TermdbDmrSuccessResponse = {
@@ -38,12 +86,23 @@ export type TermdbDmrSuccessResponse = {
 		chr: string
 		start: number
 		stop: number
-		width: number
-		max_delta_beta: number
-		/** hyper = group2 hypermethylated relative to group1; hypo = opposite */
+		/** Number of CpG sites in this DMR */
+		no_cpgs: number
+		/** Minimum FDR from the kernel-smoothed estimate across the region */
+		min_smoothed_fdr: number
+		/** Harmonic mean of individual CpG FDR-corrected p-values */
+		HMFDR: number
+		/** Maximum methylation difference (beta-scale) within the DMR */
+		maxdiff: number
+		/** Mean methylation difference across the DMR */
+		meandiff: number
+		/** hyper = case hypermethylated relative to control; hypo = opposite */
 		direction: 'hyper' | 'hypo'
-		probability: number
+		/** Comma-separated gene symbols overlapping the DMR */
+		overlapping_genes?: string | null
 	}[]
+	/** Diagnostic data: per-CpG probe means and statistics */
+	diagnostic?: DmrDiagnostic
 }
 
 export type TermdbDmrErrorResponse = {

package/src/routes/termdb.isoformAvailability.ts

@@ -0,0 +1,22 @@
+import type { RoutePayload } from './routeApi.ts'
+
+export type TermdbIsoformAvailabilityRequest = {
+	genome: string
+	dslabel: string
+	/** candidate ENST IDs to check */
+	isoforms: string[]
+}
+
+export type TermdbIsoformAvailabilityResponse = {
+	/** subset of input isoforms that have data in the HDF5 */
+	available: string[]
+}
+
+export const TermdbIsoformAvailabilityPayload: RoutePayload = {
+	request: {
+		typeId: 'TermdbIsoformAvailabilityRequest'
+	},
+	response: {
+		typeId: 'TermdbIsoformAvailabilityResponse'
+	}
+}