@sjcrh/proteinpaint-types 2.180.1 → 2.182.0

package/src/routes/termdb.violinBox.ts

@@ -0,0 +1,230 @@
+import type { RoutePayload } from './routeApi.js'
+import type { TermWrapper } from '../terms/tw.ts'
+import type { Filter } from '../filter.ts'
+import type { ErrorResponse } from './errorResponse.ts'
+import type { DescrStats } from './termdb.descrstats.ts'
+
+/** Common properties shared by both violin and box plots */
+type CommonProps = {
+	/** numeric tw to fetch numeric data. tw.q.mode must be continuous */
+	tw: TermWrapper
+	dslabel: string
+	genome: string
+	/** overlay tw for multiple violins/boxplots */
+	overlayTw?: TermWrapper
+	/** tw to divide to multiple charts */
+	divideTw?: TermWrapper
+	/** mass filter */
+	filter?: Filter
+	/** read-only invisible filter */
+	filter0?: any
+	/** TODO: Needs description FIXME delete */
+	currentGeneNames?: string[]
+	/** if true, use log scale; if false or undefined, use linear scale */
+	isLogScale?: boolean
+}
+
+/** Request type for violin plots with required violin-specific parameters */
+export type ViolinRequest = CommonProps & {
+	/** Indicates the type of chart to render */
+	plotType: 'violin'
+	/** A number representing the dimension perpendicular to the violin spread */
+	axisHeight?: number
+	/** A string representing the type of symbol used on the plot */
+	datasymbol?: string
+	/** A number representing the device's pixel ratio */
+	devicePixelRatio: number
+	/** If true, uses KDE method to build plot */
+	isKDE?: boolean
+	/** A string with two possible values: 'horizontal' or 'vertical' */
+	orientation: string
+	/** A number representing the radius of the data symbols */
+	radius: number
+	/** A number representing the right margin */
+	rightMargin?: number
+	/** Term may be scaled from regression analysis */
+	scale?: any
+	/** A number representing the width of the stroke */
+	strokeWidth?: number
+	/** A number representing the width of the SVG box */
+	svgw: number
+	/** Number of bins to build the plot. Default is 20. */
+	ticks?: number
+}
+
+/** Request type for box plots with required box-specific parameters */
+export type BoxRequest = CommonProps & {
+	/** Indicates the type of chart to render */
+	plotType: 'box'
+	/** sort plots by median value */
+	orderByMedian?: boolean
+	/** Remove outliers from the plot */
+	removeOutliers?: boolean
+	/** If true, show association tests table */
+	showAssocTests?: boolean
+}
+
+/**Unified request type for violin and boxplot - union of ViolinRequest and BoxRequest */
+export type ViolinBoxRequest = ViolinRequest | BoxRequest
+
+export type ViolinBoxResponse = ViolinResponse | BoxPlotResponse | ErrorResponse
+
+/** Type guard to check if response is an ErrorResponse */
+export function isErrorResponse(response: ViolinBoxResponse): response is ErrorResponse {
+	return 'error' in response && 'status' in response
+}
+
+/** Type guard to check if response is a BoxPlotResponse */
+export function isBoxPlotResponse(response: ViolinBoxResponse): response is BoxPlotResponse {
+	return !isErrorResponse(response) && 'charts' in response && 'descrStats' in response
+}
+
+/** Type guard to check if response is a ViolinResponse */
+export function isViolinResponse(response: ViolinBoxResponse): response is ViolinResponse {
+	return !isErrorResponse(response) && 'min' in response && 'max' in response
+}
+
+/** Violin response types */
+interface BinsEntries {
+	x0: number
+	x1: number
+	density: number
+}
+
+interface ValuesEntries {
+	id: string
+	label: string
+	value: number
+}
+
+interface PValueEntries {
+	value?: string
+	html?: string
+}
+
+type ViolinDensity = {
+	bins: BinsEntries[]
+	densityMax: number
+	densityMin: number
+}
+
+export type ViolinPlotEntry = {
+	color: string
+	chartId: string
+	density: ViolinDensity
+	label: string
+	plotValueCount: number
+	seriesId: string
+	src: string
+	summaryStats: ValuesEntries[]
+}
+
+export type ViolinResponse = {
+	bins: { [index: string]: any }
+	charts: {
+		[index: string]: {
+			chartId: string
+			plots: ViolinPlotEntry[]
+			pvalues?: PValueEntries[][]
+		}
+	}
+	min: number
+	max: number
+	uncomputableValues: { [index: string]: number }[] | null
+	descrStats?: DescrStats
+}
+
+/** Boxplot response types */
+export type BoxPlotData = {
+	w1: number | undefined
+	w2: number | undefined
+	p05: number
+	p25: number
+	p50: number
+	p75: number
+	p95: number
+	iqr: number
+	out: { value: number }[]
+}
+
+export type BoxPlotEntry = {
+	boxplot: BoxPlotData & { label: string }
+	color?: string
+	descrStats: DescrStats
+	isHidden?: boolean
+	key: string
+	seriesId?: string
+}
+
+export type BoxPlotChartEntry = {
+	chartId: string
+	plots: BoxPlotEntry[]
+	sampleCount: number
+	wilcoxon?: [{ value: string }, { value: string }, { html: string }][]
+}
+
+export type BoxPlotResponse = {
+	absMin?: number
+	absMax?: number
+	bins?: {
+		[index: string]: any
+	}
+	charts: {
+		[chartId: string]: BoxPlotChartEntry
+	}
+	descrStats: DescrStats
+	uncomputableValues: { label: string; value: number }[] | null
+}
+
+export const violinBoxPayload: RoutePayload = {
+	request: {
+		typeId: 'ViolinBoxRequest'
+	},
+	response: {
+		typeId: 'ViolinBoxResponse'
+	},
+	examples: [
+		{
+			request: {
+				body: {
+					plotType: 'violin',
+					genome: 'hg38-test',
+					dslabel: 'TermdbTest',
+					tw: {
+						term: { id: 'aaclassic_5', type: 'float' },
+						q: { mode: 'continuous' }
+					},
+					devicePixelRatio: 2,
+					svgw: 200,
+					orientation: 'horizontal',
+					datasymbol: 'rug',
+					radius: 5,
+					isLogScale: false
+				}
+			},
+			response: {
+				header: { status: 200 }
+			}
+		},
+		{
+			request: {
+				body: {
+					plotType: 'box',
+					genome: 'hg38-test',
+					dslabel: 'TermdbTest',
+					tw: {
+						term: { id: 'agedx', type: 'float' },
+						q: { mode: 'continuous' }
+					},
+					overlayTw: {
+						term: { id: 'sex', type: 'categorical' }
+					},
+					orderByMedian: true
+				}
+			},
+			response: {
+				header: { status: 200 }
+			}
+		}
+	]
+}

package/src/terms/isoformExpression.ts

@@ -0,0 +1,36 @@
+import type { PresetNumericBins, NumericBaseTerm, NumTW, RawNumTW } from '../index.ts'
+
+/*
+--------EXPORTED--------
+IsoformExpressionTerm
+IsoformExpressionTermWrapper
+*/
+
+type Isoform = {
+	kind?: 'isoform'
+	isoform: string
+	gene?: string
+	chr?: string
+	start?: number
+	stop?: number
+}
+
+type Coord = {
+	kind?: 'coord'
+	isoform?: string
+	gene?: string
+	chr: string
+	start: number
+	stop: number
+}
+
+export type IsoformExpressionTerm = NumericBaseTerm & {
+	type: 'isoformExpression'
+	bins?: PresetNumericBins
+} & (Isoform | Coord)
+
+export type IsoformExpressionTW = NumTW & { term: IsoformExpressionTerm }
+
+export type RawIsoformExpTerm = IsoformExpressionTerm & { name?: string }
+
+export type RawIsoformExpTW = RawNumTW & { term: RawIsoformExpTerm }

package/src/terms/numeric.ts

@@ -4,6 +4,7 @@ import type {
 	TermValues,
 	BaseTerm,
 	GeneExpressionTerm,
+	IsoformExpressionTerm,
 	MetaboliteIntensityTerm,
 	ProteomeAbundanceTerm,
 	DateTerm,
@@ -62,6 +63,7 @@ export type RawNumericDictTerm = NumericDictTerm & {
 export type NumericTerm =
 	| NumericDictTerm
 	| GeneExpressionTerm
+	| IsoformExpressionTerm
 	| MetaboliteIntensityTerm
 	| ProteomeAbundanceTerm
 	| DateTerm

package/src/vocab.ts

@@ -23,7 +23,6 @@ export type VocabApi = {
 	getterm: (f: any) => Term
 	getTerms: (f: any) => any
 	getTermdbConfig: () => any
-	getViolinPlotData: (args: any, _body?: any) => any
 	getAnnotatedSampleData: (args: any) => any
 	getDefaultBins: (args: any) => any
 	setTermBins(tw: TermWrapper): any