Merge pull request #382 from MoTrPAC/369_JZ_Dawg_Pac_Pheno_Data_Analysis

Connects to #369. PASS1AC-06 phenotype data analysis (initial phase).

package.json

@@ -37,6 +37,7 @@
     "react-wordcloud": "^1.2.7",
     "redux": "^4.0.1",
     "redux-thunk": "^2.3.0",
+    "simple-statistics": "^7.8.7",
     "tocbot": "^4.25.0",
     "victory": "37.0.2",
     "vis-network-react": "DinerIsmail/vis-network-react"

src/AnalysisPage/Phenotype/Components/Pass1ac-06/SummaryStatistics/categorySummaryStatistics.jsx

@@ -0,0 +1,49 @@
+import React from 'react';
+import { useSelector } from 'react-redux';
+import SectionWeightDistribution from './sectionWeightDistribution';
+import SectionLactateChange from './sectionLactateChange';
+import SectionRatWork from './sectionRatWork';
+
+/**
+ * Function component for the summary statistics category of PASS1AC-06 phenotypic data analysis
+ *
+ * @param {array} phenoData Curated phenotypic data
+ *
+ * @returns JSX element of the summary statistics category
+ */
+function CategorySummaryStatistics() {
+  const analysisState = useSelector((state) => state.analysis);
+
+  return (
+    <div className="w-100 analysis-category-content-container">
+      <h2>Summary Statistics</h2>
+      <p>
+        In this section, various summary statistics and visualizations that
+        explore key variables across the phenotypic data are presented. The
+        analysis covers weight distribution, electric shocks (both number
+        and duration), distance covered during the acute test, and lactate
+        changes due to exercise. Each variable is visualized through a
+        combination of boxplots, histograms, and density plots, broken down
+        by relevant factors such as sex, phase, and intervention group.
+        Additionally, we analyze the time taken to freeze tissues, including
+        comparisons across different groups and a detailed look at the order
+        in which tissues were frozen for each animal. These visualizations
+        help to identify patterns and trends within the phenotypic data.
+      </p>
+      {/* weight distribution section */}
+      {analysisState.pass1ac06AnalysisCategoryOptions.summaryStatistics.weight_distribution && (
+        <SectionWeightDistribution />
+      )}
+      {/* lactate change section */}
+      {analysisState.pass1ac06AnalysisCategoryOptions.summaryStatistics.lactate_change && (
+        <SectionLactateChange />
+      )}
+      {/* rat work section */}
+      {analysisState.pass1ac06AnalysisCategoryOptions.summaryStatistics.rat_work && (
+        <SectionRatWork />
+      )}
+    </div>
+  );
+}
+
+export default CategorySummaryStatistics;

src/AnalysisPage/Phenotype/Components/Pass1ac-06/SummaryStatistics/plotLactateChange.jsx

@@ -0,0 +1,113 @@
+import React, { useMemo } from 'react';
+import {
+  COLORS,
+  defaultChartOptions,
+  allBoxPlotDataByPhaseSexIntervention,
+  allScatterPlotDataByPhaseSex,
+} from '../sharedLib';
+import Chart from '../chartWrapper';
+
+/**
+ * Renders summary statistics plots for lactate change
+ *
+ * @returns JSX representation of Highcharts plots for rat work - boxplots and scatter plots
+ */
+function PlotLactateChange() {
+  // Base chart options
+  const baseChartOptions = defaultChartOptions('Intervention', 'Lactate Change', 'Lactate Change: {point.y}');
+
+  // Function to collect lactate change data for box plot
+  const getLactateChangeData = (data) => data.map((item) => parseFloat(item.lactate_change));
+  const boxPlotData = useMemo(() => allBoxPlotDataByPhaseSexIntervention(getLactateChangeData), []);
+
+  // Scatter plot data for pass1a and pass1c (both male and female)
+  const scatterData = useMemo(() => allScatterPlotDataByPhaseSex(getLactateChangeData), []);
+
+  // Highcharts options for the plots
+  const chartOptions = useMemo(() => {
+    const createChartOptions = (gender, titleText) => {
+      const allData = [
+        ...boxPlotData[`pass1a${gender}Acute`],
+        ...boxPlotData[`pass1c${gender}Acute`],
+        ...boxPlotData[`pass1a${gender}Control`],
+        ...boxPlotData[`pass1c${gender}Control`],
+        ...scatterData.pass1a[gender.toLowerCase()].map(([, y]) => y),
+        ...scatterData.pass1c[gender.toLowerCase()].map(([, y]) => y),
+      ];
+
+      const minValue = Math.min(...allData);
+      const maxValue = Math.max(...allData);
+      const padding = 0.1 * (maxValue - minValue);
+
+      return {
+        ...baseChartOptions,
+        title: {
+          align: 'left',
+          style: { fontSize: '1.5rem' },
+          text: titleText,
+        },
+        xAxis: {
+          ...baseChartOptions.xAxis,
+          categories: ['Acute', 'Control'],
+        },
+        yAxis: {
+          ...baseChartOptions.yAxis,
+          min: minValue - padding,
+          max: maxValue + padding,
+        },
+        series: [
+          {
+            name: 'PASS1A-06 Lactate Change Distribution',
+            type: 'boxplot',
+            legendSymbol: 'areaMarker',
+            data: [
+              boxPlotData[`pass1a${gender}Acute`],
+              boxPlotData[`pass1a${gender}Control`],
+            ],
+            fillColor: COLORS.pass1a.fill,
+          },
+          {
+            name: 'PASS1C-06 Lactate Change Distribution',
+            type: 'boxplot',
+            legendSymbol: 'areaMarker',
+            data: [
+              boxPlotData[`pass1c${gender}Acute`],
+              boxPlotData[`pass1c${gender}Control`],
+            ],
+            fillColor: COLORS.pass1c.fill,
+          },
+          {
+            name: 'PASS1A-06 Scatter',
+            type: 'scatter',
+            data: scatterData.pass1a[gender.toLowerCase()],
+            color: COLORS.pass1a.scatter,
+            jitter: { x: 0.1 },
+            showInLegend: false,
+          },
+          {
+            name: 'PASS1C-06 Scatter',
+            type: 'scatter',
+            data: scatterData.pass1c[gender.toLowerCase()],
+            color: COLORS.pass1c.scatter,
+            jitter: { x: 0.1 },
+            showInLegend: false,
+          },
+        ],
+      };
+    };
+
+    return {
+      male: createChartOptions('Male', 'Distribution of LACTATE CHANGE by INTERVENTION and MALE'),
+      female: createChartOptions('Female', 'Distribution of LACTATE CHANGE by INTERVENTION and FEMALE'),
+    };
+  }, [baseChartOptions, boxPlotData, scatterData]);
+
+  return (
+    <div className="col-lg-11 h-90">
+      <Chart options={chartOptions.male} className="phenotype-plot-container" />
+      <Chart options={chartOptions.female} className="phenotype-plot-container" />
+    </div>
+  );
+}
+
+export default PlotLactateChange;

src/AnalysisPage/Phenotype/Components/Pass1ac-06/SummaryStatistics/plotRatWork.jsx

@@ -0,0 +1,117 @@
+import React, { useMemo } from 'react';
+import {
+  COLORS,
+  defaultChartOptions,
+  allBoxPlotDataByPhaseSexIntervention,
+  allScatterPlotDataByPhaseSex,
+} from '../sharedLib';
+import Chart from '../chartWrapper';
+
+/**
+ * Renders summary statistics plots for rat work
+ *
+ * @returns JSX representation of Highcharts plots for rat work - boxplots and scatter plots
+ */
+function PlotRatWork() {
+  // Base chart options
+  const baseChartOptions = defaultChartOptions('Intervention', 'Work', 'Work: {point.y} joules');
+
+  // Function to collect lactate change data for box plot
+  const getRatWorkData = (data) => data.map((item) => {
+    const weight = parseInt(item.weight, 10) / 1000;
+    const distance = parseInt(item.distance, 10);
+    return weight * distance * 0.087 * 9.80665;
+  });
+  const boxPlotData = useMemo(() => allBoxPlotDataByPhaseSexIntervention(getRatWorkData), []);
+
+  // Scatter plot data for pass1a and pass1c (both male and female)
+  const scatterData = useMemo(() => allScatterPlotDataByPhaseSex(getRatWorkData), []);
+
+  // Highcharts options for the plots
+  const chartOptions = useMemo(() => {
+    const createChartOptions = (gender, titleText) => {
+      const allData = [
+        ...boxPlotData[`pass1a${gender}Acute`],
+        ...boxPlotData[`pass1c${gender}Acute`],
+        ...boxPlotData[`pass1a${gender}Control`],
+        ...boxPlotData[`pass1c${gender}Control`],
+        ...scatterData.pass1a[gender.toLowerCase()].map(([, y]) => y),
+        ...scatterData.pass1c[gender.toLowerCase()].map(([, y]) => y),
+      ];
+
+      const minValue = Math.min(...allData);
+      const maxValue = Math.max(...allData);
+      const padding = 0.1 * (maxValue - minValue);
+
+      return {
+        ...baseChartOptions,
+        title: {
+          align: 'left',
+          style: { fontSize: '1.5rem' },
+          text: titleText,
+        },
+        xAxis: {
+          ...baseChartOptions.xAxis,
+          categories: ['Acute', 'Control'],
+        },
+        yAxis: {
+          ...baseChartOptions.yAxis,
+          min: minValue - padding,
+          max: maxValue + padding,
+        },
+        series: [
+          {
+            name: 'PASS1A-06 Work Distribution',
+            type: 'boxplot',
+            legendSymbol: 'areaMarker',
+            data: [
+              boxPlotData[`pass1a${gender}Acute`],
+              boxPlotData[`pass1a${gender}Control`],
+            ],
+            fillColor: COLORS.pass1a.fill,
+          },
+          {
+            name: 'PASS1C-06 Work Distribution',
+            type: 'boxplot',
+            legendSymbol: 'areaMarker',
+            data: [
+              boxPlotData[`pass1c${gender}Acute`],
+              boxPlotData[`pass1c${gender}Control`],
+            ],
+            fillColor: COLORS.pass1c.fill,
+          },
+          {
+            name: 'PASS1A-06 Scatter',
+            type: 'scatter',
+            data: scatterData.pass1a[gender.toLowerCase()],
+            color: COLORS.pass1a.scatter,
+            jitter: { x: 0.1 },
+            showInLegend: false,
+          },
+          {
+            name: 'PASS1C-06 Scatter',
+            type: 'scatter',
+            data: scatterData.pass1c[gender.toLowerCase()],
+            color: COLORS.pass1c.scatter,
+            jitter: { x: 0.1 },
+            showInLegend: false,
+          },
+        ],
+      };
+    };
+
+    return {
+      male: createChartOptions('Male', 'Distribution of WORK by INTERVENTION and MALE'),
+      female: createChartOptions('Female', 'Distribution of WORK by INTERVENTION and FEMALE'),
+    };
+  }, [baseChartOptions, boxPlotData, scatterData]);
+
+  return (
+    <div className="col-lg-11 h-90">
+      <Chart options={chartOptions.male} className="phenotype-plot-container" />
+      <Chart options={chartOptions.female} className="phenotype-plot-container" />
+    </div>
+  );
+}
+
+export default PlotRatWork;