visualifyjs 2.5.3 → 3.0.0

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

@@ -1,172 +1,172 @@
-/*
- * @Author       : Lihao leolihao@arizona.edu
- * @Date         : 2023-12-22 22:37:23
- * @FilePath     : /visualifyjs/src/core/modules/echarts/presets/esodev.chromium.js
- * @Description  :
- * Copyright (c) 2023 by Lihao (leolihao@arizona.edu), All Rights Reserved.
- */
-const esodev_chromium = {
-	title: {
-		textStyle: {
-			fontSize: 20,
-		},
-		left: 'center',
-		top: 0,
-	},
-	animation: false,
-	legend: {
-		textStyle: {
-			fontSize: 18,
-		},
-		orient: 'horizontal',
-		right: 'center', // "top" | "bottom" | "center"
-		itemWidth: 20,
-		width: 600,
-		top: 25,
-	},
-	xAxis: {
-		name: 'UMAP 1',
-		type: 'value',
-		nameLocation: 'middle',
-		nameGap: 10,
-		nameTextStyle: {
-			fontSize: 18, // Set font size
-			fontWeight: 'bold', // Set font weight to bold
-		},
-		axisLine: { show: false },
-		axisTick: { show: false },
-		splitLine: { show: false },
-		axisLabel: { show: false },
-		//min: -20,
-		//max: 20,
-	},
-	yAxis: {
-		name: 'UMAP 2',
-		type: 'value',
-		nameLocation: 'middle',
-		nameGap: 10,
-		nameTextStyle: {
-			fontSize: 18, // Set font size
-			fontWeight: 'bold', // Set font weight to bold
-		},
-		//min: -20,
-		//max: 20,
-		axisLine: { show: false },
-		axisTick: { show: false },
-		splitLine: { show: false },
-		axisLabel: { show: false },
-	},
-	series: [],
-	grid: {
-		top: '20%',
-		bottom: '12%',
-		left: '10%',
-		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: [
-		// Inside type for X-axis
-		{
-			type: 'inside',
-			xAxisIndex: 0,
-			filterMode: 'filter',
-		},
-		// Inside type for Y-axis
-		{
-			type: 'inside',
-			yAxisIndex: 0,
-			filterMode: 'filter',
-			orient: 'vertical',
-		},
-	],
-	visualMap: {
-		min: 0,
-		max: 3,
-		dimension: 2,
-		orient: 'vertical',
-		top: 'center',
-		left: 0,
-		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 express = params.data.value[2];
-			let round_epxress = express
-				? Math.round(express * 10000) / 10000
-				: 0;
-			return `
-                    <div style="text-align: center;">
-                        ${params.data.Cell_ID} 
-                        <br/> Type: <strong>${params.data.Cell_Type} </strong>
-                        <br/> Stage: <strong>${params.data.Stage}</strong>
-                        <br/> #UMI: <strong>${params.data.UMI}</strong>
-                        <br/> #Gene: <strong>${params.data.Gene}</strong>
-                        <br/> MT%: <strong>${params.data.MT}</strong>
-                        ${
-							express !== undefined
-								? '<br/> Expression: <strong>' +
-								  round_epxress +
-								  '</strong>'
-								: ''
-						}
-                    </div>
-                `;
-		},
-	},
-	visualify: {
-		mapping: {
-			x: '2D_UMAP_1',
-			y: '2D_UMAP_2',
-			extra: {
-				Stage: 'Stage',
-				UMI: 'n_UMIs',
-				MT: 'percent_MT',
-				Gene: 'n_Genes',
-				Cell_Type: 'Cell_Type',
-				Cell_ID: 'Cell_ID',
-			},
-		},
-		seriesBy: 'Cell_Type',
-		symbolSize: 5,
-		symbol: 'circle',
-		merger: {
-			gene: {
-				item: 'Cell_ID',
-				label: 'Expression',
-				visualMap: true,
-			},
-		},
-		api_mapping: {
-			'ENS (S)': 'ens_iter_2',
-			'IM (S)': 'im_iter_2',
-			'MES (S)': 'mes_iter_2',
-			'SKM (S)': 'skm_iter_2',
-			'ENDO (S)': 'endo_iter_2',
-			'EPI (E)': 'epi_iter_2',
-			Stroma: 'stroma_iter_1',
-			Epithelium: 'epi_iter_1',
-		},
-	},
-};
-
-export default esodev_chromium;
+/*
+ * @Author       : Lihao leolihao@arizona.edu
+ * @Date         : 2023-12-22 22:37:23
+ * @FilePath     : /visualifyjs/src/core/modules/echarts/presets/esodev.chromium.js
+ * @Description  :
+ * Copyright (c) 2023 by Lihao (leolihao@arizona.edu), All Rights Reserved.
+ */
+const esodev_chromium = {
+	title: {
+		textStyle: {
+			fontSize: 20,
+		},
+		left: 'center',
+		top: 0,
+	},
+	animation: false,
+	legend: {
+		textStyle: {
+			fontSize: 18,
+		},
+		orient: 'horizontal',
+		right: 'center', // "top" | "bottom" | "center"
+		itemWidth: 20,
+		width: 600,
+		top: 25,
+	},
+	xAxis: {
+		name: 'UMAP 1',
+		type: 'value',
+		nameLocation: 'middle',
+		nameGap: 10,
+		nameTextStyle: {
+			fontSize: 18, // Set font size
+			fontWeight: 'bold', // Set font weight to bold
+		},
+		axisLine: { show: false },
+		axisTick: { show: false },
+		splitLine: { show: false },
+		axisLabel: { show: false },
+		//min: -20,
+		//max: 20,
+	},
+	yAxis: {
+		name: 'UMAP 2',
+		type: 'value',
+		nameLocation: 'middle',
+		nameGap: 10,
+		nameTextStyle: {
+			fontSize: 18, // Set font size
+			fontWeight: 'bold', // Set font weight to bold
+		},
+		//min: -20,
+		//max: 20,
+		axisLine: { show: false },
+		axisTick: { show: false },
+		splitLine: { show: false },
+		axisLabel: { show: false },
+	},
+	series: [],
+	grid: {
+		top: '20%',
+		bottom: '12%',
+		left: '10%',
+		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: [
+		// Inside type for X-axis
+		{
+			type: 'inside',
+			xAxisIndex: 0,
+			filterMode: 'filter',
+		},
+		// Inside type for Y-axis
+		{
+			type: 'inside',
+			yAxisIndex: 0,
+			filterMode: 'filter',
+			orient: 'vertical',
+		},
+	],
+	visualMap: {
+		min: 0,
+		max: 3,
+		dimension: 2,
+		orient: 'vertical',
+		top: 'center',
+		left: 0,
+		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 express = params.data.value[2];
+			let round_epxress = express
+				? Math.round(express * 10000) / 10000
+				: 0;
+			return `
+                    <div style="text-align: center;">
+                        ${params.data.Cell_ID} 
+                        <br/> Type: <strong>${params.data.Cell_Type} </strong>
+                        <br/> Stage: <strong>${params.data.Stage}</strong>
+                        <br/> #UMI: <strong>${params.data.UMI}</strong>
+                        <br/> #Gene: <strong>${params.data.Gene}</strong>
+                        <br/> MT%: <strong>${params.data.MT}</strong>
+                        ${
+							express !== undefined
+								? '<br/> Expression: <strong>' +
+								  round_epxress +
+								  '</strong>'
+								: ''
+						}
+                    </div>
+                `;
+		},
+	},
+	visualify: {
+		mapping: {
+			x: '2D_UMAP_1',
+			y: '2D_UMAP_2',
+			extra: {
+				Stage: 'Stage',
+				UMI: 'n_UMIs',
+				MT: 'percent_MT',
+				Gene: 'n_Genes',
+				Cell_Type: 'Cell_Type',
+				Cell_ID: 'Cell_ID',
+			},
+		},
+		seriesBy: 'Cell_Type',
+		symbolSize: 5,
+		symbol: 'circle',
+		merger: {
+			gene: {
+				item: 'Cell_ID',
+				label: 'Expression',
+				visualMap: true,
+			},
+		},
+		api_mapping: {
+			'ENS (S)': 'ens_iter_2',
+			'IM (S)': 'im_iter_2',
+			'MES (S)': 'mes_iter_2',
+			'SKM (S)': 'skm_iter_2',
+			'ENDO (S)': 'endo_iter_2',
+			'EPI (E)': 'epi_iter_2',
+			Stroma: 'stroma_iter_1',
+			Epithelium: 'epi_iter_1',
+		},
+	},
+};
+
+export default esodev_chromium;

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

@@ -1,130 +1,130 @@
-const esodev_codex = {
-	title: {
-		textStyle: {
-			fontSize: 20,
-		},
-		left: 'center',
-		top: 0,
-	},
-	animation: false,
-	legend: {
-		textStyle: {
-			fontSize: 18,
-		},
-		orient: 'horizontal',
-		right: 'center', // "top" | "bottom" | "center"
-		itemWidth: 20,
-		width: 600,
-		top: 25,
-	},
-	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: [
-		// Inside type for X-axis
-		{
-			type: 'inside',
-			xAxisIndex: 0,
-			filterMode: 'filter',
-		},
-		// Inside type for Y-axis
-		{
-			type: 'inside',
-			yAxisIndex: 0,
-			filterMode: 'filter',
-			orient: 'vertical',
-		},
-		{
-			type: 'slider',
-			xAxisIndex: 0,
-			filterMode: 'filter',
-		},
-		{
-			type: 'slider',
-			yAxisIndex: 0,
-			filterMode: 'filter',
-			orient: 'vertical',
-		},
-	],
-	visualMap: {
-		min: 0,
-		max: 10,
-		dimension: 2,
-		orient: 'vertical',
-		top: 'center',
-		left: 0,
-		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 express = params.data.value[2];
-			let round_epxress = express
-				? Math.round(express * 10000) / 10000
-				: 0;
-			return `
-            <div style="text-align: center;">
-                ${params.data.Cell_ID} 
-                <br/> Type: <strong>${params.data.Celltype} </strong>
-                ${
-					express !== undefined
-						? '<br/> Expression: <strong>' + round_epxress + '</strong>'
-						: ''
-				}
-            </div>
-          `;
-		},
-	},
-	visualify: {
-		mapping: {
-			x: 'X_Coord',
-			y: 'Y_Coord',
-			extra: {
-                Cell_ID: 'Cell_ID',
-				Celltype: 'Cell_Type',
-			},
-		},
-		seriesBy: 'Cell_Type',
-		symbolSize: 5,
-		symbol: 'circle',
-		merger: {
-			gene: {
-				item: 'Cell_ID',
-				label: 'Expression',
-				visualMap: true,
-			},
-		},
-	},
-};
-
-export default esodev_codex;
+const esodev_codex = {
+	title: {
+		textStyle: {
+			fontSize: 20,
+		},
+		left: 'center',
+		top: 0,
+	},
+	animation: false,
+	legend: {
+		textStyle: {
+			fontSize: 18,
+		},
+		orient: 'horizontal',
+		right: 'center', // "top" | "bottom" | "center"
+		itemWidth: 20,
+		width: 600,
+		top: 25,
+	},
+	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: [
+		// Inside type for X-axis
+		{
+			type: 'inside',
+			xAxisIndex: 0,
+			filterMode: 'filter',
+		},
+		// Inside type for Y-axis
+		{
+			type: 'inside',
+			yAxisIndex: 0,
+			filterMode: 'filter',
+			orient: 'vertical',
+		},
+		{
+			type: 'slider',
+			xAxisIndex: 0,
+			filterMode: 'filter',
+		},
+		{
+			type: 'slider',
+			yAxisIndex: 0,
+			filterMode: 'filter',
+			orient: 'vertical',
+		},
+	],
+	visualMap: {
+		min: 0,
+		max: 10,
+		dimension: 2,
+		orient: 'vertical',
+		top: 'center',
+		left: 0,
+		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 express = params.data.value[2];
+			let round_epxress = express
+				? Math.round(express * 10000) / 10000
+				: 0;
+			return `
+            <div style="text-align: center;">
+                ${params.data.Cell_ID} 
+                <br/> Type: <strong>${params.data.Celltype} </strong>
+                ${
+					express !== undefined
+						? '<br/> Expression: <strong>' + round_epxress + '</strong>'
+						: ''
+				}
+            </div>
+          `;
+		},
+	},
+	visualify: {
+		mapping: {
+			x: 'X_Coord',
+			y: 'Y_Coord',
+			extra: {
+                Cell_ID: 'Cell_ID',
+				Celltype: 'Cell_Type',
+			},
+		},
+		seriesBy: 'Cell_Type',
+		symbolSize: 5,
+		symbol: 'circle',
+		merger: {
+			gene: {
+				item: 'Cell_ID',
+				label: 'Expression',
+				visualMap: true,
+			},
+		},
+	},
+};
+
+export default esodev_codex;