visualifyjs 2.5.3 → 3.0.0

package/src/core/modules/echarts/presets/esodev.visium.js

@@ -1,123 +1,123 @@
-const esodev_visium = {
-	title: {
-		textStyle: {
-			fontSize: 20,
-		},
-		left: 'center',
-		top: 0,
-	},
-	animation: false,
-	legend: {
-		show: false,
-	},
-	xAxis: {
-		show: false,
-	},
-	yAxis: {
-		show: false,
-	},
-	series: [],
-	grid: {
-		top: '15%',
-		bottom: '12%',
-		left: '5%',
-		right: '10%',
-	},
-	// ... other default settings for charts
-	toolbox: {
-		feature: {
-			saveAsImage: {
-				show: true,
-				icon: `path://M30 20.75c-0.69 0.001-1.249 0.56-1.25 1.25v6.75h-25.5v-6.75c0-0.69-0.56-1.25-1.25-1.25s-1.25 0.56-1.25 1.25v0 8c0 0.69 0.56 1.25 1.25 1.25h28c0.69-0.001 1.249-0.56 1.25-1.25v-8c-0.001-0.69-0.56-1.249-1.25-1.25h-0zM15.116 24.885c0.012 0.012 0.029 0.016 0.041 0.027 0.103 0.099 0.223 0.18 0.356 0.239l0.008 0.003 0.001 0c0.141 0.060 0.306 0.095 0.478 0.095 0.345 0 0.657-0.139 0.883-0.365l5.001-5c0.226-0.226 0.366-0.539 0.366-0.884 0-0.691-0.56-1.251-1.251-1.251-0.345 0-0.658 0.14-0.884 0.366l-2.865 2.867v-18.982c0-0.69-0.56-1.25-1.25-1.25s-1.25 0.56-1.25 1.25v0 18.981l-2.866-2.866c-0.226-0.226-0.539-0.366-0.884-0.366-0.691 0-1.251 0.56-1.251 1.251 0 0.346 0.14 0.658 0.367 0.885v0z`,
-			},
-		},
-	},
-	dataZoom: [],
-	visualMap: {
-		min: 0,
-		max: 10,
-		dimension: 2,
-		orient: 'horizontal',
-		top: 'bottom',
-		right: 'center',
-		text: ['log2\n(tpm+1)', ''],
-		textGap: 10,
-		calculable: true,
-		inRange: {
-			color: ['#808080', '#FFA500', '#FF0000'],
-		},
-		textStyle: {
-			writingMode: 'vertical-lr',
-		},
-	},
-	tooltip: {
-		trigger: 'item',
-		axisPointer: {
-			type: 'cross',
-		},
-		formatter: (params) => {
-			let resultHtml = '';
-			for (const [key, value] of Object.entries(params.data)) {
-				if (key === 'Expression') {
-					continue;
-				}
-				if (value > 0.5) {
-					// Only show the cell type with likelihood >= 0.5
-					resultHtml += `<br>${key}: ${value.toFixed(3)}`;
-				}
-			}
-			return `
-                    <div style="text-align: center;">
-                        ${params.name}
-                        <br> Cell2Location Cell Type Likelihood 
-                        <br> (Likelihood >= 0.5)
-                        ${resultHtml}
-                    </div>
-            `;
-		},
-	},
-	visualify: {
-		mapping: {
-			x: 'X_Coord',
-			y: 'Y_Coord',
-			extra: {
-				BC: 'BC',
-				'SB-1': 'SB-1',
-				'SB-2': 'SB-2',
-				'SB-3': 'SB-3',
-				'SB-4': 'SB-4',
-				'SB-5': 'SB-5',
-				'Cil-1': 'Cil-1',
-				'Cil-2': 'Cil-2',
-				'Cy.Epi': 'Cy.Epi',
-				Fib_PG: 'Fib_PG',
-				Fib_1: 'Fib_1',
-				Fib_2: 'Fib_2',
-				Fib_3: 'Fib_3',
-				Fib_4: 'Fib_4',
-				Fib_5: 'Fib_5',
-				MF: 'MF',
-				Fib_ICC: 'Fib_ICC',
-				'Cy.Fib': 'Cy.Fib',
-				ENS_PG: 'ENS_PG',
-				Neu: 'Neu',
-				Glia: 'Glia',
-				'Cy.ENS': 'Cy.ENS',
-				Ven: 'Ven',
-				Art: 'Art',
-				Lym: 'Lym',
-				Peri: 'Peri',
-				'Cy.Peri': 'Cy.Peri',
-				SM: 'SM',
-				'Cy.SM': 'Cy.SM',
-				MS: 'MS',
-				SkM: 'SkM',
-			},
-		},
-		merger: {},
-		symbolSize: 2,
-		symbol: 'circle',
-	},
-};
-
-export default esodev_visium;
+const esodev_visium = {
+	title: {
+		textStyle: {
+			fontSize: 20,
+		},
+		left: 'center',
+		top: 0,
+	},
+	animation: false,
+	legend: {
+		show: false,
+	},
+	xAxis: {
+		show: false,
+	},
+	yAxis: {
+		show: false,
+	},
+	series: [],
+	grid: {
+		top: '15%',
+		bottom: '12%',
+		left: '5%',
+		right: '10%',
+	},
+	// ... other default settings for charts
+	toolbox: {
+		feature: {
+			saveAsImage: {
+				show: true,
+				icon: `path://M30 20.75c-0.69 0.001-1.249 0.56-1.25 1.25v6.75h-25.5v-6.75c0-0.69-0.56-1.25-1.25-1.25s-1.25 0.56-1.25 1.25v0 8c0 0.69 0.56 1.25 1.25 1.25h28c0.69-0.001 1.249-0.56 1.25-1.25v-8c-0.001-0.69-0.56-1.249-1.25-1.25h-0zM15.116 24.885c0.012 0.012 0.029 0.016 0.041 0.027 0.103 0.099 0.223 0.18 0.356 0.239l0.008 0.003 0.001 0c0.141 0.060 0.306 0.095 0.478 0.095 0.345 0 0.657-0.139 0.883-0.365l5.001-5c0.226-0.226 0.366-0.539 0.366-0.884 0-0.691-0.56-1.251-1.251-1.251-0.345 0-0.658 0.14-0.884 0.366l-2.865 2.867v-18.982c0-0.69-0.56-1.25-1.25-1.25s-1.25 0.56-1.25 1.25v0 18.981l-2.866-2.866c-0.226-0.226-0.539-0.366-0.884-0.366-0.691 0-1.251 0.56-1.251 1.251 0 0.346 0.14 0.658 0.367 0.885v0z`,
+			},
+		},
+	},
+	dataZoom: [],
+	visualMap: {
+		min: 0,
+		max: 10,
+		dimension: 2,
+		orient: 'horizontal',
+		top: 'bottom',
+		right: 'center',
+		text: ['log2\n(tpm+1)', ''],
+		textGap: 10,
+		calculable: true,
+		inRange: {
+			color: ['#808080', '#FFA500', '#FF0000'],
+		},
+		textStyle: {
+			writingMode: 'vertical-lr',
+		},
+	},
+	tooltip: {
+		trigger: 'item',
+		axisPointer: {
+			type: 'cross',
+		},
+		formatter: (params) => {
+			let resultHtml = '';
+			for (const [key, value] of Object.entries(params.data)) {
+				if (key === 'Expression') {
+					continue;
+				}
+				if (value > 0.5) {
+					// Only show the cell type with likelihood >= 0.5
+					resultHtml += `<br>${key}: ${value.toFixed(3)}`;
+				}
+			}
+			return `
+                    <div style="text-align: center;">
+                        ${params.name}
+                        <br> Cell2Location Cell Type Likelihood 
+                        <br> (Likelihood >= 0.5)
+                        ${resultHtml}
+                    </div>
+            `;
+		},
+	},
+	visualify: {
+		mapping: {
+			x: 'X_Coord',
+			y: 'Y_Coord',
+			extra: {
+				BC: 'BC',
+				'SB-1': 'SB-1',
+				'SB-2': 'SB-2',
+				'SB-3': 'SB-3',
+				'SB-4': 'SB-4',
+				'SB-5': 'SB-5',
+				'Cil-1': 'Cil-1',
+				'Cil-2': 'Cil-2',
+				'Cy.Epi': 'Cy.Epi',
+				Fib_PG: 'Fib_PG',
+				Fib_1: 'Fib_1',
+				Fib_2: 'Fib_2',
+				Fib_3: 'Fib_3',
+				Fib_4: 'Fib_4',
+				Fib_5: 'Fib_5',
+				MF: 'MF',
+				Fib_ICC: 'Fib_ICC',
+				'Cy.Fib': 'Cy.Fib',
+				ENS_PG: 'ENS_PG',
+				Neu: 'Neu',
+				Glia: 'Glia',
+				'Cy.ENS': 'Cy.ENS',
+				Ven: 'Ven',
+				Art: 'Art',
+				Lym: 'Lym',
+				Peri: 'Peri',
+				'Cy.Peri': 'Cy.Peri',
+				SM: 'SM',
+				'Cy.SM': 'Cy.SM',
+				MS: 'MS',
+				SkM: 'SkM',
+			},
+		},
+		merger: {},
+		symbolSize: 2,
+		symbol: 'circle',
+	},
+};
+
+export default esodev_visium;

package/src/core/modules/echarts/presets/mmtrbc.js

@@ -1,186 +1,186 @@
-/*
- * @Author       : Lihao leolihao@arizona.edu
- * @Date         : 2023-12-22 22:37:23
- * @FilePath     : /visualifyjs/src/core/modules/echarts/presets/mmtrbc.js
- * @Description  :
- * Copyright (c) 2023 by Lihao (leolihao@arizona.edu), All Rights Reserved.
- */
-const mmtrbc = {
-	title: {
-		text: 'MmTrBC Preset',
-		textStyle: {
-			fontFamily: 'Arial, sans-serif',
-			fontSize: 24,
-			color: 'black',
-			margin: '0 0 20px 0',
-		},
-		left: 'center',
-		top: 0,
-	},
-	tooltip: {
-		trigger: 'item',
-		axisPointer: {
-			type: 'cross',
-		},
-		formatter: (params) => {
-			let express = params.data.value[2];
-			let round_epxress = express
-				? Math.round(express * 10000) / 10000
-				: 0;
-
-			let round = (num, n = 2) =>
-				Math.round(num * Math.pow(10, n)) / Math.pow(10, n);
-
-			return ` ${params.data.Cell_ID} <br/> 
-					Type: ${params.seriesName} <br/> 
-					UMI: ${params.data.UMI ?? 'not found'} <br/>
-					FMT: ${round(params.data.Frac_MT, 5) ?? 'not found'} <br/>
-					${express !== undefined ? 'Expression: ' + round_epxress : ''} `;
-		},
-	},
-	legend: {
-		top: 30,
-		textStyle: {
-			fontFamily: 'Arial, sans-serif',
-			fontSize: 18,
-		},
-		type: 'scroll',
-		orient: 'horizontal',
-		right: 'center',
-		width: '80%',
-	},
-	xAxis: {
-		name: 'TSNE-2',
-		type: 'value',
-		axisLabel: false,
-		nameGap: 10,
-		nameLocation: 'middle',
-		axisTick: false,
-		splitLine: false,
-		nameTextStyle: {
-			fontSize: '18',
-			fontWeight: 'bold',
-		},
-	},
-	yAxis: {
-		name: 'TSNE-1',
-		type: 'value',
-		axisLabel: false,
-		nameGap: 10,
-		nameLocation: 'middle',
-		axisTick: false,
-		splitLine: false,
-		nameTextStyle: {
-			fontSize: '18',
-			fontWeight: 'bold',
-		},
-	},
-	series: [],
-	grid: {
-		containLabel: true,
-		left: '5%',
-		right: '13%',
-		top: '13%',
-		bottom: '13%',
-	},
-	// ... other default settings for charts
-	toolbox: {
-		feature: {
-			saveAsImage: {
-				show: true,
-				icon: `path://M30 20.75c-0.69 0.001-1.249 0.56-1.25 1.25v6.75h-25.5v-6.75c0-0.69-0.56-1.25-1.25-1.25s-1.25 0.56-1.25 1.25v0 8c0 0.69 0.56 1.25 1.25 1.25h28c0.69-0.001 1.249-0.56 1.25-1.25v-8c-0.001-0.69-0.56-1.249-1.25-1.25h-0zM15.116 24.885c0.012 0.012 0.029 0.016 0.041 0.027 0.103 0.099 0.223 0.18 0.356 0.239l0.008 0.003 0.001 0c0.141 0.060 0.306 0.095 0.478 0.095 0.345 0 0.657-0.139 0.883-0.365l5.001-5c0.226-0.226 0.366-0.539 0.366-0.884 0-0.691-0.56-1.251-1.251-1.251-0.345 0-0.658 0.14-0.884 0.366l-2.865 2.867v-18.982c0-0.69-0.56-1.25-1.25-1.25s-1.25 0.56-1.25 1.25v0 18.981l-2.866-2.866c-0.226-0.226-0.539-0.366-0.884-0.366-0.691 0-1.251 0.56-1.251 1.251 0 0.346 0.14 0.658 0.367 0.885v0z`,
-			},
-		},
-	},
-	dataZoom: [
-		{ type: 'inside', xAxisIndex: 0 },
-		{ type: 'inside', yAxisIndex: 0 },
-		{
-			type: 'slider',
-			xAxisIndex: 0,
-		},
-		{ type: 'slider', yAxisIndex: 0, orient: 'vertical' },
-	],
-	visualMap: {
-		min: 0,
-		max: 8,
-		dimension: 2,
-		orient: 'vertical',
-		top: 'center',
-		right: 35,
-		text: ['log2\n(tpm+1)', ''],
-		textGap: 10,
-		calculable: true,
-		inRange: {
-			color: [
-				'rgb(43, 120, 182)',
-				'rgb(247, 126, 11)',
-				'rgb(59, 160, 30)',
-				'rgb(206, 37, 41)',
-				'rgb(143, 103, 191)',
-				'rgb(134, 86, 74)',
-			],
-		},
-		textStyle: {
-			writingMode: 'vertical-lr',
-		},
-	},
-	visualify: {
-		colors_for_celltype: [
-			{
-				name: 'BC-1',
-				color: 'rgb(43, 120, 182)',
-				symbol: 'circle',
-			},
-			{
-				name: 'BC-2',
-				color: 'rgb(247, 126, 11)',
-				symbol: 'circle',
-			},
-			{
-				name: 'BC-Sec',
-				color: 'rgb(59, 160, 30)',
-				symbol: 'circle',
-			},
-			{
-				name: 'BC-Sq',
-				color: 'rgb(206, 37, 41)',
-				symbol: 'circle',
-			},
-			{
-				name: 'BC-Mes',
-				color: 'rgb(143, 103, 191)',
-				symbol: 'circle',
-			},
-			{
-				name: 'BC-Pro',
-				color: 'rgb(134, 86, 74)',
-				symbol: 'circle',
-			},
-		],
-		mapping: {
-			extra: {
-				UMI: 'N_UMI',
-				N_gene: 'N_gene',
-				Frac_MT: 'Frac_MT',
-				Cell_ID: 'Cell_ID',
-			},
-		},
-		exclude: ['BC-Mes', 'BC-NE', 'BC-Im'],
-		seriesBy: 'Cell_Type',
-		symbolSize: 5,
-		symbol: 'circle',
-		merger: {
-			gene: {
-				item: 'Cell_ID',
-				label: 'Expression',
-				visualMap: true,
-			},
-		},
-		filter: {
-			Expression: '>-1',
-		},
-	},
-};
-
-export default mmtrbc;
+/*
+ * @Author       : Lihao leolihao@arizona.edu
+ * @Date         : 2023-12-22 22:37:23
+ * @FilePath     : /visualifyjs/src/core/modules/echarts/presets/mmtrbc.js
+ * @Description  :
+ * Copyright (c) 2023 by Lihao (leolihao@arizona.edu), All Rights Reserved.
+ */
+const mmtrbc = {
+	title: {
+		text: 'MmTrBC Preset',
+		textStyle: {
+			fontFamily: 'Arial, sans-serif',
+			fontSize: 24,
+			color: 'black',
+			margin: '0 0 20px 0',
+		},
+		left: 'center',
+		top: 0,
+	},
+	tooltip: {
+		trigger: 'item',
+		axisPointer: {
+			type: 'cross',
+		},
+		formatter: (params) => {
+			let express = params.data.value[2];
+			let round_epxress = express
+				? Math.round(express * 10000) / 10000
+				: 0;
+
+			let round = (num, n = 2) =>
+				Math.round(num * Math.pow(10, n)) / Math.pow(10, n);
+
+			return ` ${params.data.Cell_ID} <br/> 
+					Type: ${params.seriesName} <br/> 
+					UMI: ${params.data.UMI ?? 'not found'} <br/>
+					FMT: ${round(params.data.Frac_MT, 5) ?? 'not found'} <br/>
+					${express !== undefined ? 'Expression: ' + round_epxress : ''} `;
+		},
+	},
+	legend: {
+		top: 30,
+		textStyle: {
+			fontFamily: 'Arial, sans-serif',
+			fontSize: 18,
+		},
+		type: 'scroll',
+		orient: 'horizontal',
+		right: 'center',
+		width: '80%',
+	},
+	xAxis: {
+		name: 'TSNE-2',
+		type: 'value',
+		axisLabel: false,
+		nameGap: 10,
+		nameLocation: 'middle',
+		axisTick: false,
+		splitLine: false,
+		nameTextStyle: {
+			fontSize: '18',
+			fontWeight: 'bold',
+		},
+	},
+	yAxis: {
+		name: 'TSNE-1',
+		type: 'value',
+		axisLabel: false,
+		nameGap: 10,
+		nameLocation: 'middle',
+		axisTick: false,
+		splitLine: false,
+		nameTextStyle: {
+			fontSize: '18',
+			fontWeight: 'bold',
+		},
+	},
+	series: [],
+	grid: {
+		containLabel: true,
+		left: '5%',
+		right: '13%',
+		top: '13%',
+		bottom: '13%',
+	},
+	// ... other default settings for charts
+	toolbox: {
+		feature: {
+			saveAsImage: {
+				show: true,
+				icon: `path://M30 20.75c-0.69 0.001-1.249 0.56-1.25 1.25v6.75h-25.5v-6.75c0-0.69-0.56-1.25-1.25-1.25s-1.25 0.56-1.25 1.25v0 8c0 0.69 0.56 1.25 1.25 1.25h28c0.69-0.001 1.249-0.56 1.25-1.25v-8c-0.001-0.69-0.56-1.249-1.25-1.25h-0zM15.116 24.885c0.012 0.012 0.029 0.016 0.041 0.027 0.103 0.099 0.223 0.18 0.356 0.239l0.008 0.003 0.001 0c0.141 0.060 0.306 0.095 0.478 0.095 0.345 0 0.657-0.139 0.883-0.365l5.001-5c0.226-0.226 0.366-0.539 0.366-0.884 0-0.691-0.56-1.251-1.251-1.251-0.345 0-0.658 0.14-0.884 0.366l-2.865 2.867v-18.982c0-0.69-0.56-1.25-1.25-1.25s-1.25 0.56-1.25 1.25v0 18.981l-2.866-2.866c-0.226-0.226-0.539-0.366-0.884-0.366-0.691 0-1.251 0.56-1.251 1.251 0 0.346 0.14 0.658 0.367 0.885v0z`,
+			},
+		},
+	},
+	dataZoom: [
+		{ type: 'inside', xAxisIndex: 0 },
+		{ type: 'inside', yAxisIndex: 0 },
+		{
+			type: 'slider',
+			xAxisIndex: 0,
+		},
+		{ type: 'slider', yAxisIndex: 0, orient: 'vertical' },
+	],
+	visualMap: {
+		min: 0,
+		max: 8,
+		dimension: 2,
+		orient: 'vertical',
+		top: 'center',
+		right: 35,
+		text: ['log2\n(tpm+1)', ''],
+		textGap: 10,
+		calculable: true,
+		inRange: {
+			color: [
+				'rgb(43, 120, 182)',
+				'rgb(247, 126, 11)',
+				'rgb(59, 160, 30)',
+				'rgb(206, 37, 41)',
+				'rgb(143, 103, 191)',
+				'rgb(134, 86, 74)',
+			],
+		},
+		textStyle: {
+			writingMode: 'vertical-lr',
+		},
+	},
+	visualify: {
+		colors_for_celltype: [
+			{
+				name: 'BC-1',
+				color: 'rgb(43, 120, 182)',
+				symbol: 'circle',
+			},
+			{
+				name: 'BC-2',
+				color: 'rgb(247, 126, 11)',
+				symbol: 'circle',
+			},
+			{
+				name: 'BC-Sec',
+				color: 'rgb(59, 160, 30)',
+				symbol: 'circle',
+			},
+			{
+				name: 'BC-Sq',
+				color: 'rgb(206, 37, 41)',
+				symbol: 'circle',
+			},
+			{
+				name: 'BC-Mes',
+				color: 'rgb(143, 103, 191)',
+				symbol: 'circle',
+			},
+			{
+				name: 'BC-Pro',
+				color: 'rgb(134, 86, 74)',
+				symbol: 'circle',
+			},
+		],
+		mapping: {
+			extra: {
+				UMI: 'N_UMI',
+				N_gene: 'N_gene',
+				Frac_MT: 'Frac_MT',
+				Cell_ID: 'Cell_ID',
+			},
+		},
+		exclude: ['BC-Mes', 'BC-NE', 'BC-Im'],
+		seriesBy: 'Cell_Type',
+		symbolSize: 5,
+		symbol: 'circle',
+		merger: {
+			gene: {
+				item: 'Cell_ID',
+				label: 'Expression',
+				visualMap: true,
+			},
+		},
+		filter: {
+			Expression: '>-1',
+		},
+	},
+};
+
+export default mmtrbc;