@sjcrh/proteinpaint-types 2.180.1 → 2.182.0

package/dist/termdb.boxplot.js

@@ -1,11 +0,0 @@
-import {
-  boxplotPayload,
-  validBoxPlotRequest,
-  validBoxPlotResponse
-} from "./chunk-XAGXFLSH.js";
-import "./chunk-YNHC5SXO.js";
-export {
-  boxplotPayload,
-  validBoxPlotRequest,
-  validBoxPlotResponse
-};

package/dist/termdb.violin.js

@@ -1,11 +0,0 @@
-import {
-  validViolinRequest,
-  validViolinResponse,
-  violinPayload
-} from "./chunk-R7BNDCKV.js";
-import "./chunk-YNHC5SXO.js";
-export {
-  validViolinRequest,
-  validViolinResponse,
-  violinPayload
-};

package/src/routes/termdb.boxplot.ts

@@ -1,164 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-import type { TermWrapper } from '../terms/tw.ts'
-import type { Filter } from '../filter.ts'
-import type { DescrStats } from './termdb.descrstats.ts'
-
-/**Args set in Termdb vocab and from mass box plot */
-export type BoxPlotRequest = {
-	/** Args set in TermVocab */
-	/** term1 or term */
-	tw: TermWrapper
-	genome: string
-	dslabel: string
-	/** if true, only return positive values */
-	isLogScale: boolean
-	/** sort plots by median value */
-	orderByMedian: boolean
-	removeOutliers?: boolean
-	/** If true, show association tests table */
-	showAssocTests?: boolean
-	/** term2 */
-	overlayTw?: TermWrapper
-	/** term0 */
-	divideTw?: TermWrapper
-	filter?: Filter
-	filter0?: any
-}
-
-export type BoxPlotResponse = {
-	/** Absolute min value for all plots */
-	absMin?: number
-	/** Absolute max value for all plots */
-	absMax?: number
-	/** Bins for overlay and/or divide terms */
-	bins?: {
-		[index: string]: any
-	}
-	/** Charts data. chartId corresponds the divide by term value*/
-	charts: {
-		[chartId: string]: BoxPlotChartEntry
-	}
-	/** Descriptive statistics for the entire response */
-	descrStats: DescrStats
-	/** Categories not shown in the final plot */
-	uncomputableValues: { label: string; value: number }[] | null
-	error?: any
-}
-
-// chart containing a set of boxplots
-export type BoxPlotChartEntry = {
-	/** Chart ID */
-	chartId: string
-	/** Boxplot data within the chart */
-	plots: BoxPlotEntry[]
-	/** Number of samples represented in the chart */
-	sampleCount: number
-	/** Wilcoxon test results for the chart formatted
-	 * for #dom/table.js */
-	wilcoxon?: [{ value: string }, { value: string }, { html: string }][]
-}
-
-// individual boxplot
-export type BoxPlotEntry = {
-	boxplot: BoxPlotData & { label: string }
-	/** color matching the value/category color */
-	color?: string
-	descrStats: DescrStats
-	/** Pertains to an uncomputable term value and
-	 * whether or not the plot is hidden by default */
-	isHidden?: boolean
-	key: string
-	/** Usually the same as key, but determined by the tw */
-	seriesId?: string
-}
-
-export type BoxPlotData = {
-	/** Min/1st whisker value */
-	w1: number | undefined
-	/** Max/2nd whisker value */
-	w2: number | undefined
-	/** 5% */
-	p05: number
-	/** 25% */
-	p25: number
-	/** 50%, median */
-	p50: number
-	/** 75% */
-	p75: number
-	/** 95% */
-	p95: number
-	/** Interquartile region */
-	iqr: number
-	/** Outliers */
-	out: { value: number }[]
-}
-
-export type BoxPlotDescrStatsEntry = {
-	/** 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
-}
-
-export const boxplotPayload: RoutePayload = {
-	request: {
-		typeId: 'BoxPlotRequest'
-	},
-	response: {
-		typeId: 'BoxPlotResponse'
-	},
-	examples: [
-		{
-			request: {
-				body: {
-					tw: {
-						term: { id: 'subcohort', type: 'categorical' },
-						values: [{ key: 'ABC', label: 'ABC' }]
-					},
-					genome: 'hg38-test',
-					dslabel: 'TermdbTest',
-					orderByMedian: true
-				}
-			},
-			response: {
-				body: {
-					absMin: 0,
-					absMax: 100,
-					plots: [
-						{
-							boxplot: {
-								label: 'ABC',
-								w1: 0,
-								w2: 100,
-								p05: 0,
-								p25: 25,
-								p50: 50,
-								p75: 75,
-								p95: 100,
-								iqr: 50,
-								out: [101, 102, 106]
-							},
-							color: 'blue',
-							descrStats: [
-								{ id: 'total', label: 'Total', value: 100 },
-								{ id: 'min', label: 'Min', value: 0 },
-								{ id: 'p25', label: '25%', value: 25 },
-								{ id: 'median', label: 'Median', value: 50 },
-								{ id: 'mean', label: 'Mean', value: 50 },
-								{ id: 'p75', label: '75%', value: 75 },
-								{ id: 'max', label: 'Max', value: 100 },
-								{ id: 'sd', label: 'SD', value: 0 },
-								{ id: 'variance', label: 'Variance', value: 0 },
-								{ id: 'iqr', label: 'IQR', value: 50 }
-							],
-							key: 'ABC'
-						}
-					],
-					uncomputableValues: [{ label: 'uncomputable-test', value: 1 }]
-				}
-			}
-		}
-	]
-}

package/src/routes/termdb.violin.ts

@@ -1,163 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-import type { Filter } from '../filter.ts'
-import type { ErrorResponse } from './errorResponse.ts'
-
-export type ViolinRequest = {
-	/** A number representing the dimension perpendicular to the violin spread
-	 * (the height of the axis) */
-	axisHeight: number
-	/** ?? TODO: Needs description */
-	currentGeneNames: string[]
-	/** A string representing the type of symbol used on the plot, which can be
-	 * either 'circles' or 'rugs' */
-	datasymbol: string
-	/** A number representing the device's pixel ratio, which may be used for
-	 * rendering quality adjustments */
-	devicePixelRatio: number
-	/** optional overlay tw, will generate multiple violin plots */
-	overlayTw?: any
-	/** optional divide tw, will generate multiple charts, each of which will contain violin plots */
-	divideTw?: any
-	/** Reference label (i.e. short label) for the ds */
-	dslabel: string
-	/** optional mass filter */
-	filter?: Filter
-	/** optional read-only invisible filter TODO GdcFilter0 */
-	filter0?: any
-	/** Reference label */
-	genome: string
-	/** If true, uses KDE method to build plot. Otherwise a histogram is rendered */
-	isKDE: boolean
-	/** A string with two possible values: 'horizontal' or 'vertical',
-	 * indicating the orientation of the chart, either horizontal or vertical */
-	orientation: 'horizontal' | 'vertical'
-	/** A number representing the radius of the data symbols rendered on the plot */
-	radius: number
-	/** A number representing the right margin of the chart or plot */
-	rightMargin: number
-	/** Term may be scaled from regression analysis. Equivalent of term.q.scale */
-	scale?: any
-	/** A number representing the width of the stroke used to generate the data symbols
-	 * (data symbols are rendered on the server side) */
-	strokeWidth: number
-	/** A number representing the width of the SVG (Scalable Vector Graphics) box, used for
-	 * rendering the chart */
-	svgw: number
-	/** Number of bins to build the plot. Default is 20. */
-	ticks: number
-	/** main tw to fetch numeric data to show in violin */
-	tw: any
-	/** A string representing a unit of measurement (e.g., 'log' for log scale) */
-	unit: string
-}
-
-/** ?? TODO: Needs description */
-interface BinsEntries {
-	x0: number
-	x1: number
-	density: number
-}
-
-/** ?? TODO: Needs description */
-interface ValuesEntries {
-	id: string
-	label: string
-	value: number
-}
-
-/** Computed in wilcoxon to show in table */
-interface PValueEntries {
-	value?: string
-	html?: string
-}
-
-/** ?? TODO: Needs description */
-type ViolinDensity = {
-	bins: BinsEntries[]
-	densityMax: number
-	densityMin: number
-}
-
-export type ViolinPlotEntry = {
-	/** Color to render */
-	color: string
-	chartId: string
-	density: ViolinDensity
-	/** Text for label */
-	label: string
-	/** Number of samples/cases/patients/etc. */
-	plotValueCount: number
-	/** Corresponds to the tw.$id */
-	seriesId: string
-	/** Plot image to display */
-	src: string
-	/** Descriptive stats (i.e. min, max, sd, etc.) */
-	summaryStats: ValuesEntries[]
-}
-
-export type ViolinResponse = ValidResponse | ErrorResponse
-
-type ValidResponse = {
-	/** Bins used for each term
-	 * Used for listing samples, filtering, etc.*/
-	bins: { [index: string]: any }
-	charts: {
-		[index: string]: {
-			chartId: string
-			plots: ViolinPlotEntry[]
-			pvalues?: PValueEntries[][]
-		}
-	}
-	/** Absolute min value for all plots */
-	min: number
-	/** Absolute max value for all plots */
-	max: number
-	uncomputableValues: { [index: string]: number }[] | null
-}
-
-export const violinPayload: RoutePayload = {
-	request: {
-		typeId: 'ViolinRequest'
-	},
-	response: {
-		typeId: 'ViolinResponse'
-	},
-	examples: [
-		{
-			request: {
-				body: {
-					genome: 'hg38-test',
-					dslabel: 'TermdbTest',
-					embedder: 'localhost',
-					devicePixelRatio: 2.200000047683716,
-					maxThickness: 150,
-					screenThickness: 1218,
-					filter: {
-						type: 'tvslst',
-						in: true,
-						join: '',
-						lst: [
-							{
-								tag: 'cohortFilter',
-								type: 'tvs',
-								tvs: { term: { id: 'subcohort', type: 'categorical' }, values: [{ key: 'ABC', label: 'ABC' }] }
-							}
-						]
-					},
-					svgw: 227.27272234672367,
-					orientation: 'horizontal',
-					datasymbol: 'bean',
-					radius: 5,
-					strokeWidth: 0.2,
-					axisHeight: 60,
-					rightMargin: 50,
-					unit: 'abs',
-					termid: 'agedx'
-				}
-			},
-			response: {
-				header: { status: 200 }
-			}
-		}
-	]
-}