@sjcrh/proteinpaint-types 2.177.0 → 2.178.0

package/dist/termdb.chat2.js

@@ -0,0 +1,13 @@
+import {
+  validChatRequest,
+  validChatResponse
+} from "./chunk-GAYJUXNZ.js";
+import {
+  ChatPayload
+} from "./chunk-FRXRNCDV.js";
+import "./chunk-YNHC5SXO.js";
+export {
+  ChatPayload,
+  validChatRequest,
+  validChatResponse
+};

package/dist/termdb.cluster.js

@@ -2,7 +2,7 @@ import {
   termdbClusterPayload,
   validTermdbClusterRequest,
   validTermdbClusterResponse
-} from "./chunk-Q6MWNJ2V.js";
+} from "./chunk-NRV6MPRM.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbClusterPayload,

package/dist/termdb.descrstats.js

@@ -2,7 +2,7 @@ import {
   descrStatsPayload,
   validDescrStatsRequest,
   validDescrStatsResponse
-} from "./chunk-63OD34W2.js";
+} from "./chunk-UWAVSKMD.js";
 import "./chunk-YNHC5SXO.js";
 export {
   descrStatsPayload,

package/dist/termdb.diffMeth.js

@@ -0,0 +1,11 @@
+import {
+  diffMethPayload,
+  validDiffMethRequest,
+  validDiffMethResponse
+} from "./chunk-4DCPDZW4.js";
+import "./chunk-YNHC5SXO.js";
+export {
+  diffMethPayload,
+  validDiffMethRequest,
+  validDiffMethResponse
+};

package/dist/termdb.dmr.js

@@ -0,0 +1,11 @@
+import {
+  TermdbDmrPayload,
+  validTermdbDmrRequest,
+  validTermdbDmrResponse
+} from "./chunk-CYQDO4FX.js";
+import "./chunk-YNHC5SXO.js";
+export {
+  TermdbDmrPayload,
+  validTermdbDmrRequest,
+  validTermdbDmrResponse
+};

package/dist/termdb.numericcategories.js

@@ -2,7 +2,7 @@ import {
   numericCategoriesPayload,
   validNumericCategoriesRequest,
   validNumericCategoriesResponse
-} from "./chunk-5KF6Z3GL.js";
+} from "./chunk-CX2Y673E.js";
 import "./chunk-YNHC5SXO.js";
 export {
   numericCategoriesPayload,

package/dist/termdb.percentile.js

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

package/dist/termdb.singlecellData.js

@@ -2,7 +2,7 @@ import {
   termdbSingleCellDataPayload,
   validTermdbSingleCellDataRequest,
   validTermdbSingleCellDataResponse
-} from "./chunk-4ZMQ5CTL.js";
+} from "./chunk-NIEACU6R.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbSingleCellDataPayload,

package/dist/termdb.termsbyids.js

@@ -2,7 +2,7 @@ import {
   termsByIdsPayload,
   validTermsByIdsRequest,
   validTermsByIdsResponse
-} from "./chunk-7WEVNKAM.js";
+} from "./chunk-HZEV7D5E.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termsByIdsPayload,

package/dist/termdb.topTermsByType.js

@@ -2,7 +2,7 @@ import {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,
   validTermdbTopTermsByTypeResponse
-} from "./chunk-URHI6FFP.js";
+} from "./chunk-UFYKXOY2.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbTopTermsByTypePayload,

package/dist/termdb.topVariablyExpressedGenes.js

@@ -2,7 +2,7 @@ import {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,
   validTermdbTopVariablyExpressedGenesResponse
-} from "./chunk-W7UCAYSF.js";
+} from "./chunk-FQYNRDHB.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbTopVariablyExpressedGenesPayload,

package/dist/termdb.violin.js

@@ -2,7 +2,7 @@ import {
   validViolinRequest,
   validViolinResponse,
   violinPayload
-} from "./chunk-44LN7YTE.js";
+} from "./chunk-PHRILOVX.js";
 import "./chunk-YNHC5SXO.js";
 export {
   validViolinRequest,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.177.0",
+  "version": "2.178.0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -1,4 +1,6 @@
 import type { Mclass } from './Mclass.ts'
+import type { BaseTerm } from './terms/term.ts'
+import type { CategoryKey } from './terms/termCollection.ts'
 import type { WSImage } from './routes/samplewsimages.ts'
 import type { WSISample } from './routes/wsisamples.ts'
 import type { SaveWSIAnnotationRequest } from './routes/saveWSIAnnotation.ts'
@@ -694,6 +696,17 @@ export type MetaboliteIntensityQueryNative = {
 
 export type MetaboliteIntensityQuery = MetaboliteIntensityQueryNative
 
+export type WholeProteomeAbundanceQuery = {
+	/** document structure */
+	file: string
+	samples?: number[]
+	/** _proteins,used to dynamically built cache of protein names to speed up search */
+	_proteins?: string[]
+	get?: (param: any) => void
+	find?: (param: string[]) => void
+	bins?: { [index: string]: any }
+}
+
 /** the geneExpression query
 three possibilities
 { src: 'native', file }
@@ -853,6 +866,8 @@ export type SingleCellQuery = {
 	DEgenes?: SingleCellDEgeneGdc
 	/** supplies per-sample images. will create a new tab on the ui. one image per sample */
 	images?: SCImages
+	/** Created on mds.init() from colorMap and alias within each plot. */
+	terms?: object[]
 }
 
 type SCImages = {
@@ -967,6 +982,21 @@ type Mds3Queries = {
 		file: string
 		// in case a genome may have more than 1 geneset dbs, here may specify name of db that this result is based on */
 	}
+	/** dna methylation beta value matrix
+	 */
+	dnaMethylation?: {
+		/** path to h5 file */
+		file: string
+		/** dna methylation unit (e.g. 'Average Beta Value') */
+		unit: string
+		/** promoter-by-sample matrix, values are average M-value */
+		promoter?: {
+			/** path to h5 file */
+			file: string
+			/** unit label for promoter values (e.g. 'Average M-value') */
+			unit: string
+		}
+	}
 	rnaseqGeneCount?: RnaseqGeneCount
 	/** Used to create the top mutated genes UI in the gene
 	 * set edit ui and data requests. */
@@ -978,6 +1008,10 @@ type Mds3Queries = {
 		src: 'native'
 		file: string
 	}
+	proteome?: {
+		/** whole proteome abundance */
+		whole?: WholeProteomeAbundanceQuery
+	}
 	singleCell?: SingleCellQuery
 	singleSampleGenomeQuantification?: SingleSampleGenomeQuantification
 	singleSampleGbtk?: SingleSampleGbtk
@@ -1607,18 +1641,18 @@ keep this setting here for reason of:
 	isTermVisible?: (clientAuthResult: any, ids: string) => boolean
 	hiddenIds?: string[]
 	getAdditionalFilter?: (__protected__: any, term: any) => Filter | undefined
-	/** collections of numeric dictionary terms that are related and can be used together in some plots
-	 */
-	numericTermCollections?: NumericTermCollection[]
+	/** collections of dictionary terms (numeric or categorical) that are related and can be used together in some plots */
+	termCollections?: TermCollection[]
 }
 
-type NumericTermCollection = {
-	/** collection id */
-	id?: string
-	/** human readable name for this collection, may be as collection id if missing */
+type TermCollectionBase = {
+	/** human readable name as well as unique identifier for this collection */
 	name: string
-	/** array of dictionary numeric term ids belonging to this collection */
+	/** array of dictionary term ids belonging to this collection */
 	termIds: string[]
+	/** full term objects corresponding to termIds[]; populated by server on dataset init,
+	 * sent to client so fill() can resolve member term names without extra requests */
+	termlst?: BaseTerm[]
 	/** array of branch term ids belonging to this collection,
 	 * may be used as state.tree.expandedTermIds[] option to termdb appInit() */
 	branchIds: string[]
@@ -1634,6 +1668,18 @@ type NumericTermCollection = {
 	}[]
 }
 
+type NumericTermCollection = TermCollectionBase & {
+	type: 'numeric'
+}
+
+type CategoricalTermCollection = TermCollectionBase & {
+	type: 'categorical'
+	/** category values to filter on; hydrated form uses CategoryKey[] */
+	categoryKeys: CategoryKey[]
+}
+
+type TermCollection = NumericTermCollection | CategoricalTermCollection
+
 type SampleType = {
 	name: string
 	plural_name: string
@@ -1960,6 +2006,7 @@ export type Mds3 = BaseMds & {
 	validate_filter0?: (f: any) => void
 	ssm2canonicalisoform?: GdcApi
 	variant2samples?: Variant2Samples
+	scatterplots?: Scatterplots
 	/** disables switching to genomic mode for the protein view mds3 tk of this ds
 	works by preventing block gmmode menu from showing "genomic" option
 	is only passed via mds3 adhoc ds copy, but not termdbConfig

package/src/index.ts

@@ -40,12 +40,14 @@ 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.chat.ts'
+export * from './routes/termdb.chat2.ts'
 export * from './routes/termdb.cluster.ts'
 export * from './routes/termdb.cohort.summary.ts'
 export * from './routes/termdb.cohorts.ts'
 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.numericcategories.ts'
 export * from './routes/termdb.percentile.ts'
 export * from './routes/termdb.runChart.ts'
@@ -73,6 +75,7 @@ export * from './terms/numeric.ts'
 export * from './terms/geneVariant.ts'
 export * from './terms/geneExpression.ts'
 export * from './terms/metaboliteIntensity.ts'
+export * from './terms/wholeProteomeAbundance.ts'
 export * from './terms/qualitative.ts'
 export * from './terms/singleCellCellType.ts'
 export * from './terms/singleCellGeneExpression.ts'
@@ -80,6 +83,7 @@ export * from './terms/snp.ts'
 export * from './terms/snps.ts'
 export * from './terms/samplelst.ts'
 export * from './terms/ssGSEA.ts'
+export * from './terms/dnaMethylation.ts'
 export * from './terms/q.ts'
 export * from './terms/term.ts'
 export * from './terms/termCollection.ts'

package/src/routes/grin2.ts

@@ -1,13 +1,5 @@
-/** General GRIN2 route
- * This route handles the GRIN2 analysis for any non-GDC data.
- * It processes the incoming data structure via PP's existing filter infrastructure
- * and returns the same structured results as GDC-GRIN2.
- * Specifically it will return a sortable table of top mutated genes and
- * a static PNG manhattan-like plot of the -log10(q-value).
- * We allow the user to customize the snvindel, CNV, and fusion filtering options.
- */
-
 import type { RoutePayload } from './routeApi.js'
+import type { Filter } from '../filter.ts'
 
 /** GRIN2 request */
 export type GRIN2Request = {
@@ -49,8 +41,8 @@ export type GRIN2Request = {
 	/** Bin size for Manhattan plot histogram bin size. Used in the calculation of dynamic y-axis capping process (default: 10) */
 	binSize: number
 
-	/** Filter from existing PP infrastructure */
-	filter?: any // Filter object passed to get_samples(filter, ds)
+	/** pp filter */
+	filter?: Filter
 
 	/** Options for filtering SNV/indel file content */
 	snvindelOptions?: {
@@ -66,6 +58,8 @@ export type GRIN2Request = {
 		fivePrimeFlankSize?: number
 		/** Number of bases to include as 3' flank around the mutation position */
 		threePrimeFlankSize?: number
+		/** MAF filter object (tvslst) to filter mutations by allele frequency */
+		mafFilter?: Filter
 	}
 
 	/** Options for filtering CNV file content */

package/src/routes/{termdb.chat.ts → termdb.chat2.ts}

@@ -11,9 +11,14 @@ export type ChatRequest = {
 	__protected__?: any
 }
 
-type HtmlResponse = {
+export type TextResponse = {
+	type: 'text'
+	/** Plain text message to display in the chat */
+	text: string
+}
+export type HtmlResponse = {
 	type: 'html'
-	/** for display only */
+	/** Pre-approved HTML from the dataset JSON resources array */
 	html: string
 }
 export type PlotResponse = {
@@ -22,9 +27,20 @@ export type PlotResponse = {
 	/** Specifies what action to take e.g. Summary plot or no action. Will add more chart types later */
 }
 
-export type LlmConfig = { provider: 'SJ' | 'ollama'; api: string; modelName: string }
+export type LlmConfig = {
+	provider: 'SJ' | 'ollama'
+	api: string
+	modelName: string
+	embeddingModelName: string
+	/** Whether to load the embedding model locally (via transformers.js) or call a remote API. Defaults to 'local'. */
+	embeddingModelAccess?: 'local' | 'api'
+	/** Smaller model to use for LLM classification fallback. Defaults to modelName if not set. */
+	classifierModelName?: string
+	/** Log verbose debug output (e.g. raw embedding arrays) to the terminal. Defaults to false. */
+	verbose?: boolean
+}
 
-export type ChatResponse = HtmlResponse | PlotResponse
+export type ChatResponse = TextResponse | HtmlResponse | PlotResponse
 
 export const ChatPayload: RoutePayload = {
 	request: {
@@ -90,23 +106,34 @@ export type DbValue = {
 }
 
 export type ClassificationType =
-	| html_type
-	| plot_type /** Variable containing the type of action the UI needs to take */
-
-export type html_type = {
-	/** When type == html, display the string in the html field */
-	type: 'html'
-	/** The message to be dislayed on the chatbot UI */
-	html: string
-}
+	| plot_type
+	| resource_type
+	| none_type /** Variable containing the type of action the UI needs to take */
 
 export type plot_type = {
 	/** When type == plot, show the corresponding plot in the plot field */
 	type: 'plot'
-	/** The type of plot to be displayed on the UI. */
-	plot: 'summary' | 'dge' | 'none' | 'survival' | 'matrix' | 'sampleScatter'
+	/** The type of plot to be displayed on the UI.
+	 *  Standard categories are listed; datasets may define additional custom categories. */
+	plot: 'summary' | 'dge' | 'survival' | 'matrix' | 'sampleScatter'
 }
 
+export type resource_type = {
+	/** When type == resource, invoke the resource agent to return a matching resource link */
+	type: 'resource'
+}
+
+export type none_type = {
+	/** When type == none, the query did not match any known category */
+	type: 'none'
+}
+
+/** Top-level classification returned by classifyQuery: plot or notplot (subtype determined separately by plot.ts) */
+export type QueryClassification = { type: 'plot' } | { type: 'notplot' }
+
+/** Specific plot type returned by classifyPlotType in plot.ts */
+export type PlotType = 'summary' | 'dge' | 'survival' | 'matrix' | 'samplescatter'
+
 export type DEType = {
 	/** Name of group1 which is an array of filter terms */
 	group1: FilterTerm[]

package/src/routes/termdb.cluster.ts

@@ -4,6 +4,7 @@ import type { Filter } from '../filter.ts'
 import type { Term } from '../terms/term.ts'
 import type { GeneExpressionTW } from '../terms/geneExpression.ts'
 import type { MetaboliteIntensityTW } from '../terms/metaboliteIntensity.ts'
+import type { WholeProteomeAbundanceTW } from '../terms/wholeProteomeAbundance.ts'
 import type { NumericTW } from '../terms/numeric.ts'
 
 export type Gene = {
@@ -48,6 +49,15 @@ export type TermdbClusterRequestMetabolite = TermdbClusterRequestBase & {
 	zScoreTransformation?: string
 }
 
+export type TermdbClusterRequestWholeProteomeAbundance = TermdbClusterRequestBase & {
+	/** Data type */
+	dataType: 'wholeProteomeAbundance'
+	/** List of terms */
+	terms: WholeProteomeAbundanceTW[]
+	/** perform z-score transformation on values */
+	zScoreTransformation?: string
+}
+
 export type TermdbClusterRequestNumericDictTerm = TermdbClusterRequestBase & {
 	/** Data type */
 	dataType: 'numericDictTerm'
@@ -61,6 +71,7 @@ export type TermdbClusterRequest =
 	| TermdbClusterRequestGeneExpression
 	| TermdbClusterRequestMetabolite
 	| TermdbClusterRequestNumericDictTerm
+	| TermdbClusterRequestWholeProteomeAbundance
 
 export type Hclust = {
 	merge: { n1: number; n2: number }[]

package/src/routes/termdb.diffMeth.ts

@@ -0,0 +1,49 @@
+import type { RoutePayload } from './routeApi.js'
+
+export type DiffMethRequest = {
+	/** Genome build name */
+	genome: string
+	/** Dataset label */
+	dslabel: string
+	/** Object containing two arrays of samples for differential methylation analysis */
+	samplelst: any
+	/** Minimum non-NA samples required per group (default 3) */
+	min_samples_per_group?: number
+	/** Term for confounding variable 1 (if present) */
+	tw?: any
+	/** Term for confounding variable 2 (if present) */
+	tw2?: any
+	/** Option to return early with actual number of samples with methylation values */
+	preAnalysis?: boolean
+}
+
+export type DiffMethResponse = {
+	/** Array of promoter-level differential methylation results */
+	data: DiffMethDataEntry[]
+	/** Effective sample size for group 1 */
+	sample_size1: number
+	/** Effective sample size for group 2 */
+	sample_size2: number
+}
+
+export type DiffMethDataEntry = {
+	/** ENCODE CRE promoter ID (e.g. EH38E3756858) */
+	promoter_id: string
+	/** Gene symbol(s) associated with the promoter (comma-separated if multiple) */
+	gene_name: string
+	/** M-value difference (positive = hypermethylated in cases) */
+	fold_change: number
+	/** Raw p-value from moderated t-test */
+	original_p_value: number
+	/** FDR-adjusted p-value (Benjamini-Hochberg) */
+	adjusted_p_value: number
+}
+
+export const diffMethPayload: RoutePayload = {
+	request: {
+		typeId: 'DiffMethRequest'
+	},
+	response: {
+		typeId: 'DiffMethResponse'
+	}
+}

package/src/routes/termdb.dmr.ts

@@ -0,0 +1,47 @@
+import type { Filter } from '../filter.ts'
+import type { RoutePayload } from './routeApi.ts'
+
+export type TermdbDmrRequest = {
+	genome: string
+	dslabel: string
+	/** list of samples from each group */
+	group1: Sample[]
+	group2: Sample[]
+	/** query region */
+	chr: string
+	start: number
+	stop: number
+	// todo more params
+	filter?: Filter
+	__protected__?: any
+}
+
+type Sample = {
+	sampleId: number | string
+	sample: string
+}
+
+export type TermdbDmrSuccessResponse = {
+	status: 'ok'
+	dmrs: {
+		chr: string
+		start: number
+		stop: number
+		// todo more stats
+	}[]
+}
+
+export type TermdbDmrErrorResponse = {
+	error: string
+}
+
+export type TermdbDmrResponse = TermdbDmrSuccessResponse | TermdbDmrErrorResponse
+
+export const TermdbDmrPayload: RoutePayload = {
+	request: {
+		typeId: 'TermdbDmrRequest'
+	},
+	response: {
+		typeId: 'TermdbDmrResponse'
+	}
+}

package/src/routes/termdb.singlecellData.ts

@@ -44,8 +44,10 @@ export type TermdbSingleCellDataRequest = {
 	key: plot.name, value: column name
 	if missing, use default setting of the plot
 	*/
-	colorBy?: { [key: string]: string }
+	// colorBy?: { [key: string]: string }
+	colorBy?: string
 	colorMap?: { [key: string]: string }
+	singleCellPlot?: any
 }
 
 export type HasdataResponse = {

package/src/terms/dnaMethylation.ts

@@ -0,0 +1,19 @@
+import type { NumericBaseTerm, NumericQ, PresetNumericBins, NumTW, RawNumTW } from './numeric.ts'
+
+export type DnaMethylationQ = NumericQ & { dt?: number }
+
+export type DnaMethylationTerm = NumericBaseTerm & {
+	/** term.id: plan to be concatenated string value "chr:start-stop" */
+	/** term.name: can be user-assigned */
+	type: 'dnaMethylation'
+	chr: string
+	start: number
+	stop: number
+	bins?: PresetNumericBins
+}
+
+export type RawDnaMethylationTerm = DnaMethylationTerm & { name?: string }
+
+export type DnaMethylationTW = NumTW & { term: DnaMethylationTerm }
+
+export type RawDnaMethylationTW = RawNumTW & { term: RawDnaMethylationTerm }

package/src/terms/numeric.ts

@@ -5,8 +5,11 @@ import type {
 	BaseTerm,
 	GeneExpressionTerm,
 	MetaboliteIntensityTerm,
+	WholeProteomeAbundanceTerm,
 	DateTerm,
-	SsGSEATerm
+	SsGSEATerm,
+	DnaMethylationTerm,
+	SingleCellGeneExpressionTerm
 } from '../index.ts'
 
 export type RawRegularBin = Partial<RegularNumericBinConfig> & { preferredBins?: string }
@@ -56,7 +59,15 @@ export type RawNumericDictTerm = NumericDictTerm & {
 	id?: string
 }
 
-export type NumericTerm = NumericDictTerm | GeneExpressionTerm | MetaboliteIntensityTerm | DateTerm | SsGSEATerm
+export type NumericTerm =
+	| NumericDictTerm
+	| GeneExpressionTerm
+	| MetaboliteIntensityTerm
+	| WholeProteomeAbundanceTerm
+	| DateTerm
+	| SsGSEATerm
+	| DnaMethylationTerm
+	| SingleCellGeneExpressionTerm
 
 export type StartUnboundedBin = {
 	// where possible, assign a concrete value (true) when it is known in advance,

package/src/terms/singleCellCellType.ts

@@ -4,7 +4,7 @@ export type SingleCellCellTypeTerm = BaseTerm & {
 	type: 'singleCellCellType'
 	/** the cell types may be also cell attributes like CNV, Fusion, etc */
 	/** single cell terms require a sample to read the term values, they are associated with a sample */
-	sample: string
+	sample: object
 	/** the plot defined in the dataset contains a column with the term values for the sample, it needs to be passed to read the sample values */
 	plot: string
 	groupsetting: TermGroupSetting

package/src/terms/singleCellGeneExpression.ts

@@ -1,26 +1,32 @@
-import type { TermWrapper } from './tw.ts'
-import type { TermSettingInstance } from '../termsetting.ts'
-import type { NumericTerm, NumericQ } from './numeric.ts'
+// import type { BaseTerm } from '../index.ts'
+import type { PresetNumericBins, NumericBaseTerm, NumTW, RawNumTW } from '../index.ts'
 
-/*
---------EXPORTED--------
-GeneExpressionQ
-GeneExpressionTermWrapper
-GeneExpressionTermSettingInstance
-
-*/
+type Gene = {
+	kind?: 'gene'
+	gene: string
+	chr?: string
+	start?: number
+	stop?: number
+}
 
-export type SingleCellGeneExpressionTW = TermWrapper & {
-	q: NumericQ
-	term: SingleCellGeneExpressionTerm
+type Coord = {
+	kind?: 'coord'
+	gene?: string
+	chr: string
+	start: number
+	stop: number
 }
 
-export type SingleCellGeneExpressionTerm = NumericTerm & {
+export type SingleCellGeneExpressionTerm = NumericBaseTerm & {
+	type: 'singleCellGeneExpression'
 	gene: string
 	sample: string
-}
+	unit: string
+	bins?: PresetNumericBins
+} & (Gene | Coord)
 
-export type SingleCellGeneExpressionTermSettingInstance = TermSettingInstance & {
-	q: NumericQ
-	term: SingleCellGeneExpressionTerm
-}
+export type SingleCellGeneExpressionTermTW = NumTW & { term: SingleCellGeneExpressionTerm }
+
+export type RawSingleCellGeneExpTerm = SingleCellGeneExpressionTerm & { name?: string }
+
+export type RawSingleCellGeneExpTW = RawNumTW & { term: RawSingleCellGeneExpTerm }