From e45954933be0df822238b7889a42199296447eae Mon Sep 17 00:00:00 2001
From: Jimmy Zhen <jzhen@stanford.edu>
Date: Thu, 2 May 2024 16:20:47 -0700
Subject: [PATCH 1/5] Add timecourse trajectory links to data-viz tool

---
 .../GraphicalClustering/Pass1bLandscapeTissues/ADRNL.jsx     | 5 +++++
 .../GraphicalClustering/Pass1bLandscapeTissues/BAT.jsx       | 5 +++++
 .../GraphicalClustering/Pass1bLandscapeTissues/BLOOD.jsx     | 5 +++++
 .../GraphicalClustering/Pass1bLandscapeTissues/COLON.jsx     | 5 +++++
 .../GraphicalClustering/Pass1bLandscapeTissues/CORTEX.jsx    | 5 +++++
 .../GraphicalClustering/Pass1bLandscapeTissues/HEART.jsx     | 5 +++++
 .../GraphicalClustering/Pass1bLandscapeTissues/HIPPOC.jsx    | 5 +++++
 .../GraphicalClustering/Pass1bLandscapeTissues/KIDNEY.jsx    | 5 +++++
 .../GraphicalClustering/Pass1bLandscapeTissues/LIVER.jsx     | 5 +++++
 .../GraphicalClustering/Pass1bLandscapeTissues/LUNG.jsx      | 5 +++++
 .../GraphicalClustering/Pass1bLandscapeTissues/PLASMA.jsx    | 5 +++++
 .../GraphicalClustering/Pass1bLandscapeTissues/SKM_GN.jsx    | 5 +++++
 .../GraphicalClustering/Pass1bLandscapeTissues/SKM_VL.jsx    | 5 +++++
 .../GraphicalClustering/Pass1bLandscapeTissues/SMLINT.jsx    | 5 +++++
 .../GraphicalClustering/Pass1bLandscapeTissues/SPLEEN.jsx    | 5 +++++
 .../GraphicalClustering/Pass1bLandscapeTissues/WAT_SC.jsx    | 5 +++++
 16 files changed, 80 insertions(+)

diff --git a/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/ADRNL.jsx b/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/ADRNL.jsx
index d93eb3b8..f6b680f0 100644
--- a/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/ADRNL.jsx
+++ b/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/ADRNL.jsx
@@ -153,6 +153,11 @@ function GraphicalAnalysisAdrenal() {
                   <img src={`${imageURL}/figure_6.png`} width="100%" alt="" />
                   <img src={`${imageURL}/figure_7.png`} width="100%" alt="" />
                 </p>
+                <DataVizLink
+                  title="timecourse"
+                  tissue="Adrenal"
+                  plotType="Trajectories"
+                />
                 <hr />
               </div>
               <div className="section level4">
diff --git a/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/BAT.jsx b/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/BAT.jsx
index c7b20973..3d6dfe12 100644
--- a/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/BAT.jsx
+++ b/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/BAT.jsx
@@ -154,6 +154,11 @@ function GraphicalAnalysisBrownAdipose() {
                   <img src={`${imageURL}/figure_7.png`} width="100%" alt="" />
                   <img src={`${imageURL}/figure_8.png`} width="100%" alt="" />
                 </p>
+                <DataVizLink
+                  title="timecourse"
+                  tissue="Brown Adipose"
+                  plotType="Trajectories"
+                />
                 <hr />
               </div>
               <div className="section level4">
diff --git a/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/BLOOD.jsx b/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/BLOOD.jsx
index b36321db..74e6b65b 100644
--- a/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/BLOOD.jsx
+++ b/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/BLOOD.jsx
@@ -147,6 +147,11 @@ function GraphicalAnalysisBlood() {
                   <img src={`${imageURL}/figure_6.png`} width="100%" alt="" />
                   <img src={`${imageURL}/figure_7.png`} width="100%" alt="" />
                 </p>
+                <DataVizLink
+                  title="timecourse"
+                  tissue="Blood RNA"
+                  plotType="Trajectories"
+                />
                 <hr />
               </div>
               <div className="section level4">
diff --git a/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/COLON.jsx b/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/COLON.jsx
index c4ccf1d5..7f997455 100644
--- a/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/COLON.jsx
+++ b/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/COLON.jsx
@@ -149,6 +149,11 @@ function GraphicalAnalysisColon() {
                   <img src={`${imageURL}/figure_6.png`} width="100%" alt="" />
                   <img src={`${imageURL}/figure_7.png`} width="100%" alt="" />
                 </p>
+                <DataVizLink
+                  title="timecourse"
+                  tissue="Colon"
+                  plotType="Trajectories"
+                />
                 <hr />
               </div>
               <div className="section level4">
diff --git a/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/CORTEX.jsx b/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/CORTEX.jsx
index 38f44238..28f93edb 100644
--- a/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/CORTEX.jsx
+++ b/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/CORTEX.jsx
@@ -150,6 +150,11 @@ function GraphicalAnalysisCortex() {
                   <img src={`${imageURL}/figure_7.png`} width="100%" alt="" />
                   <img src={`${imageURL}/figure_8.png`} width="100%" alt="" />
                 </p>
+                <DataVizLink
+                  title="timecourse"
+                  tissue="Cortex"
+                  plotType="Trajectories"
+                />
                 <hr />
               </div>
               <div className="section level4">
diff --git a/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/HEART.jsx b/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/HEART.jsx
index 7932b2b3..357a67b7 100644
--- a/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/HEART.jsx
+++ b/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/HEART.jsx
@@ -149,6 +149,11 @@ function GraphicalAnalysisHeart() {
                   <img src={`${imageURL}/figure_8.png`} width="100%" alt="" />
                   <img src={`${imageURL}/figure_9.png`} width="100%" alt="" />
                 </p>
+                <DataVizLink
+                  title="timecourse"
+                  tissue="Heart"
+                  plotType="Trajectories"
+                />
                 <hr />
               </div>
               <div className="section level4">
diff --git a/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/HIPPOC.jsx b/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/HIPPOC.jsx
index 866b1978..174f2694 100644
--- a/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/HIPPOC.jsx
+++ b/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/HIPPOC.jsx
@@ -154,6 +154,11 @@ function GraphicalAnalysisHippocampus() {
                   <img src={`${imageURL}/figure_7.png`} width="100%" alt="" />
                   <img src={`${imageURL}/figure_8.png`} width="100%" alt="" />
                 </p>
+                <DataVizLink
+                  title="timecourse"
+                  tissue="Hippocampus"
+                  plotType="Trajectories"
+                />
                 <hr />
               </div>
               <div className="section level4">
diff --git a/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/KIDNEY.jsx b/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/KIDNEY.jsx
index fbe50a64..0edf1f6b 100644
--- a/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/KIDNEY.jsx
+++ b/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/KIDNEY.jsx
@@ -145,6 +145,11 @@ function GraphicalAnalysisKidney() {
                   <img src={`${imageURL}/figure_8.png`} width="100%" alt="" />
                   <img src={`${imageURL}/figure_9.png`} width="100%" alt="" />
                 </p>
+                <DataVizLink
+                  title="timecourse"
+                  tissue="Kidney"
+                  plotType="Trajectories"
+                />
                 <hr />
               </div>
               <div className="section level4">
diff --git a/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/LIVER.jsx b/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/LIVER.jsx
index 4805e42e..d1a76fea 100644
--- a/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/LIVER.jsx
+++ b/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/LIVER.jsx
@@ -145,6 +145,11 @@ function GraphicalAnalysisLiver() {
                   <img src={`${imageURL}/figure_8.png`} width="100%" alt="" />
                   <img src={`${imageURL}/figure_9.png`} width="100%" alt="" />
                 </p>
+                <DataVizLink
+                  title="timecourse"
+                  tissue="Liver"
+                  plotType="Trajectories"
+                />
                 <hr />
               </div>
               <div className="section level4">
diff --git a/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/LUNG.jsx b/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/LUNG.jsx
index b9343560..9d259d99 100644
--- a/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/LUNG.jsx
+++ b/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/LUNG.jsx
@@ -141,6 +141,11 @@ function GraphicalAnalysisLung() {
                   <img src={`${imageURL}/figure_8.png`} width="100%" alt="" />
                   <img src={`${imageURL}/figure_9.png`} width="100%" alt="" />
                 </p>
+                <DataVizLink
+                  title="timecourse"
+                  tissue="Lung"
+                  plotType="Trajectories"
+                />
                 <hr />
               </div>
               <div className="section level4">
diff --git a/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/PLASMA.jsx b/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/PLASMA.jsx
index b1ee741c..ee05dd3f 100644
--- a/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/PLASMA.jsx
+++ b/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/PLASMA.jsx
@@ -143,6 +143,11 @@ function GraphicalAnalysisPlasma() {
                   <img src={`${imageURL}/figure_6.png`} width="100%" alt="" />
                   <img src={`${imageURL}/figure_7.png`} width="100%" alt="" />
                 </p>
+                <DataVizLink
+                  title="timecourse"
+                  tissue="Plasma"
+                  plotType="Trajectories"
+                />
                 <hr />
               </div>
             </div>
diff --git a/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/SKM_GN.jsx b/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/SKM_GN.jsx
index 1ef7107a..a4013801 100644
--- a/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/SKM_GN.jsx
+++ b/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/SKM_GN.jsx
@@ -155,6 +155,11 @@ function GraphicalAnalysisGastrocnemius() {
                   <img src={`${imageURL}/figure_8.png`} width="100%" alt="" />
                   <img src={`${imageURL}/figure_9.png`} width="100%" alt="" />
                 </p>
+                <DataVizLink
+                  title="timecourse"
+                  tissue="Gastrocnemius"
+                  plotType="Trajectories"
+                />
                 <hr />
               </div>
               <div className="section level4">
diff --git a/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/SKM_VL.jsx b/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/SKM_VL.jsx
index 05b3cb62..16ab0432 100644
--- a/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/SKM_VL.jsx
+++ b/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/SKM_VL.jsx
@@ -147,6 +147,11 @@ function GraphicalAnalysisVastusLateralis() {
                   <img src={`${imageURL}/figure_6.png`} width="100%" alt="" />
                   <img src={`${imageURL}/figure_7.png`} width="100%" alt="" />
                 </p>
+                <DataVizLink
+                  title="timecourse"
+                  tissue="Vastus Lateralis"
+                  plotType="Trajectories"
+                />
                 <hr />
               </div>
               <div className="section level4">
diff --git a/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/SMLINT.jsx b/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/SMLINT.jsx
index f87f8261..6e0adb8f 100644
--- a/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/SMLINT.jsx
+++ b/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/SMLINT.jsx
@@ -147,6 +147,11 @@ function GraphicalAnalysisSmallIntestine() {
                   <img src={`${imageURL}/figure_6.png`} width="100%" alt="" />
                   <img src={`${imageURL}/figure_7.png`} width="100%" alt="" />
                 </p>
+                <DataVizLink
+                  title="timecourse"
+                  tissue="Small Intestine"
+                  plotType="Trajectories"
+                />
                 <hr />
               </div>
               <div className="section level4">
diff --git a/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/SPLEEN.jsx b/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/SPLEEN.jsx
index 6d65fd91..3f75696e 100644
--- a/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/SPLEEN.jsx
+++ b/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/SPLEEN.jsx
@@ -143,6 +143,11 @@ function GraphicalAnalysisSpleen() {
                   <img src={`${imageURL}/figure_6.png`} width="100%" alt="" />
                   <img src={`${imageURL}/figure_7.png`} width="100%" alt="" />
                 </p>
+                <DataVizLink
+                  title="timecourse"
+                  tissue="Spleen"
+                  plotType="Trajectories"
+                />
                 <hr />
               </div>
               <div className="section level4">
diff --git a/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/WAT_SC.jsx b/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/WAT_SC.jsx
index 9499d14d..adff66fc 100644
--- a/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/WAT_SC.jsx
+++ b/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/WAT_SC.jsx
@@ -149,6 +149,11 @@ function GraphicalAnalysisWhiteAdipose() {
                   <img src={`${imageURL}/figure_8.png`} width="100%" alt="" />
                   <img src={`${imageURL}/figure_9.png`} width="100%" alt="" />
                 </p>
+                <DataVizLink
+                  title="timecourse"
+                  tissue="White Adipose"
+                  plotType="Trajectories"
+                />
                 <hr />
               </div>
               <div className="section level4">

From 6e1f9c0ea7aabb08e5d0ab18644e449d6985d755 Mon Sep 17 00:00:00 2001
From: Jimmy Zhen <jzhen@stanford.edu>
Date: Thu, 2 May 2024 16:22:58 -0700
Subject: [PATCH 2/5] Add prop to support data-viz plots with small minimum
 cluster size

---
 .../GraphicalClustering/Pass1bLandscapeTissues/HYPOTH.jsx       | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/HYPOTH.jsx b/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/HYPOTH.jsx
index 6119b421..0a0e86af 100644
--- a/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/HYPOTH.jsx
+++ b/src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/HYPOTH.jsx
@@ -40,6 +40,7 @@ function GraphicalAnalysisHypothalamus() {
                 title="trajectory"
                 tissue="Hypothalamus"
                 plotType="Tree"
+                minClusterSize={1}
               />
             </div>
             <div className="section level3">
@@ -55,6 +56,7 @@ function GraphicalAnalysisHypothalamus() {
                 title="cluster"
                 tissue="Hypothalamus"
                 plotType="Histogram"
+                minClusterSize={1}
               />
             </div>
           </div>

From 78bf2f3bfdc09b5f709b501d38bc483d0c4ad376 Mon Sep 17 00:00:00 2001
From: Jimmy Zhen <jzhen@stanford.edu>
Date: Thu, 2 May 2024 16:24:54 -0700
Subject: [PATCH 3/5] Add support for more params to be used for linking out to
 data-viz portal

---
 .../components/dataVizLink.jsx                | 22 +++++++++++++++++--
 1 file changed, 20 insertions(+), 2 deletions(-)

diff --git a/src/AnalysisPage/GraphicalClustering/components/dataVizLink.jsx b/src/AnalysisPage/GraphicalClustering/components/dataVizLink.jsx
index 539fcc63..0202c5fd 100644
--- a/src/AnalysisPage/GraphicalClustering/components/dataVizLink.jsx
+++ b/src/AnalysisPage/GraphicalClustering/components/dataVizLink.jsx
@@ -1,8 +1,21 @@
 import React from 'react';
 import PropTypes from 'prop-types';
 
-function DataVizLink({ title, tissue, plotType }) {
-  const url = `https://data-viz.motrpac-data.org/?tissues[${tissue}]=1&plot_type=${plotType}&topk=10`;
+function DataVizLink({ title, tissue, plotType, minClusterSize }) {
+  let topkStr = '';
+  let minClusterSizeStr = '';
+
+  // include 'topk' param for non-trajectory plots
+  if (plotType !== 'Trajectories') {
+    topkStr = '&topk=10';
+  }
+
+  // include 'min_cluster_size' param if minClusterSize is provided
+  if (minClusterSize && typeof (minClusterSize) === 'number') {
+    minClusterSizeStr = `&min_cluster_size=${minClusterSize}`;
+  }
+
+  const url = `https://data-viz.motrpac-data.org/?tissues[${tissue}]=1&plot_type=${plotType}${topkStr}${minClusterSizeStr}`;
 
   return (
     <p className="data-visualization-link-container text-center">
@@ -23,6 +36,11 @@ DataVizLink.propTypes = {
   title: PropTypes.string.isRequired,
   tissue: PropTypes.string.isRequired,
   plotType: PropTypes.string.isRequired,
+  minClusterSize: PropTypes.number,
+};
+
+DataVizLink.defaultProps = {
+  minClusterSize: null,
 };
 
 export default DataVizLink;

From 0023fad7b79043e189d66aaa0ffe7ba1feeb621f Mon Sep 17 00:00:00 2001
From: Jimmy Zhen <jzhen@stanford.edu>
Date: Thu, 2 May 2024 16:44:14 -0700
Subject: [PATCH 4/5] Add timecourse trajectory visualization links to
 graphical analysis reports

---
 .../GraphicalClustering/Pass1bMitoTissues/ADRNL.jsx          | 5 +++++
 .../GraphicalClustering/Pass1bMitoTissues/BAT.jsx            | 5 +++++
 .../GraphicalClustering/Pass1bMitoTissues/BLOOD.jsx          | 5 +++++
 .../GraphicalClustering/Pass1bMitoTissues/COLON.jsx          | 5 +++++
 .../GraphicalClustering/Pass1bMitoTissues/HEART.jsx          | 5 +++++
 .../GraphicalClustering/Pass1bMitoTissues/KIDNEY.jsx         | 5 +++++
 .../GraphicalClustering/Pass1bMitoTissues/LIVER.jsx          | 5 +++++
 .../GraphicalClustering/Pass1bMitoTissues/LUNG.jsx           | 5 +++++
 .../GraphicalClustering/Pass1bMitoTissues/SKM_GN.jsx         | 5 +++++
 .../GraphicalClustering/Pass1bMitoTissues/SKM_VL.jsx         | 5 +++++
 .../GraphicalClustering/Pass1bMitoTissues/SMLINT.jsx         | 5 +++++
 .../GraphicalClustering/Pass1bMitoTissues/SPLEEN.jsx         | 5 +++++
 .../GraphicalClustering/Pass1bMitoTissues/WAT_SC.jsx         | 5 +++++
 13 files changed, 65 insertions(+)

diff --git a/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/ADRNL.jsx b/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/ADRNL.jsx
index 7778f580..3b1c04b8 100644
--- a/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/ADRNL.jsx
+++ b/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/ADRNL.jsx
@@ -150,6 +150,11 @@ function MitoGraphicalAnalysisAdrenal() {
                   <img src={`${imageURL}/figure_7.png`} width="100%" alt="" />
                   <img src={`${imageURL}/figure_8.png`} width="100%" alt="" />
                 </p>
+                <DataVizLink
+                  title="timecourse"
+                  tissue="Adrenal"
+                  plotType="Trajectories"
+                />
                 <hr />
               </div>
               <div className="section level4">
diff --git a/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/BAT.jsx b/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/BAT.jsx
index 340107d3..637eb7b9 100644
--- a/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/BAT.jsx
+++ b/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/BAT.jsx
@@ -150,6 +150,11 @@ function MitoGraphicalAnalysisBrownAdipose() {
                   <img src={`${imageURL}/figure_7.png`} width="100%" alt="" />
                   <img src={`${imageURL}/figure_8.png`} width="100%" alt="" />
                 </p>
+                <DataVizLink
+                  title="timecourse"
+                  tissue="Brown Adipose"
+                  plotType="Trajectories"
+                />
                 <hr />
               </div>
               <div className="section level4">
diff --git a/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/BLOOD.jsx b/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/BLOOD.jsx
index fe23567a..4f9e020b 100644
--- a/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/BLOOD.jsx
+++ b/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/BLOOD.jsx
@@ -150,6 +150,11 @@ function MitoGraphicalAnalysisBlood() {
                   <img src={`${imageURL}/figure_7.png`} width="100%" alt="" />
                   <img src={`${imageURL}/figure_8.png`} width="100%" alt="" />
                 </p>
+                <DataVizLink
+                  title="timecourse"
+                  tissue="Blood RNA"
+                  plotType="Trajectories"
+                />
                 <hr />
               </div>
               <div className="section level4">
diff --git a/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/COLON.jsx b/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/COLON.jsx
index 9acaf1a8..f6db2fbf 100644
--- a/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/COLON.jsx
+++ b/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/COLON.jsx
@@ -146,6 +146,11 @@ function MitoGraphicalAnalysisColon() {
                   <img src={`${imageURL}/figure_7.png`} width="100%" alt="" />
                   <img src={`${imageURL}/figure_8.png`} width="100%" alt="" />
                 </p>
+                <DataVizLink
+                  title="timecourse"
+                  tissue="Colon"
+                  plotType="Trajectories"
+                />
                 <hr />
               </div>
               <div className="section level4">
diff --git a/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/HEART.jsx b/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/HEART.jsx
index 16c28822..cc3bf366 100644
--- a/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/HEART.jsx
+++ b/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/HEART.jsx
@@ -147,6 +147,11 @@ function MitoGraphicalAnalysisHeart() {
                   <img src={`${imageURL}/figure_8.png`} width="100%" alt="" />
                   <img src={`${imageURL}/figure_9.png`} width="100%" alt="" />
                 </p>
+                <DataVizLink
+                  title="timecourse"
+                  tissue="Heart"
+                  plotType="Trajectories"
+                />
                 <hr />
               </div>
               <div className="section level4">
diff --git a/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/KIDNEY.jsx b/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/KIDNEY.jsx
index da0823b1..e365a3ac 100644
--- a/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/KIDNEY.jsx
+++ b/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/KIDNEY.jsx
@@ -146,6 +146,11 @@ function MitoGraphicalAnalysisKidney() {
                   <img src={`${imageURL}/figure_7.png`} width="100%" alt="" />
                   <img src={`${imageURL}/figure_8.png`} width="100%" alt="" />
                 </p>
+                <DataVizLink
+                  title="timecourse"
+                  tissue="Kidney"
+                  plotType="Trajectories"
+                />
                 <hr />
               </div>
               <div className="section level4">
diff --git a/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/LIVER.jsx b/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/LIVER.jsx
index fa46f328..a4cc4661 100644
--- a/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/LIVER.jsx
+++ b/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/LIVER.jsx
@@ -147,6 +147,11 @@ function MitoGraphicalAnalysisLiver() {
                   <img src={`${imageURL}/figure_8.png`} width="100%" alt="" />
                   <img src={`${imageURL}/figure_9.png`} width="100%" alt="" />
                 </p>
+                <DataVizLink
+                  title="timecourse"
+                  tissue="Liver"
+                  plotType="Trajectories"
+                />
                 <hr />
               </div>
               <div className="section level4">
diff --git a/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/LUNG.jsx b/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/LUNG.jsx
index e016b439..1dd31c99 100644
--- a/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/LUNG.jsx
+++ b/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/LUNG.jsx
@@ -137,6 +137,11 @@ function MitoGraphicalAnalysisLung() {
                   <img src={`${imageURL}/figure_6.png`} width="100%" alt="" />
                   <img src={`${imageURL}/figure_7.png`} width="100%" alt="" />
                 </p>
+                <DataVizLink
+                  title="timecourse"
+                  tissue="Lung"
+                  plotType="Trajectories"
+                />
                 <hr />
               </div>
               <div className="section level4">
diff --git a/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/SKM_GN.jsx b/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/SKM_GN.jsx
index 5d594789..293f3126 100644
--- a/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/SKM_GN.jsx
+++ b/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/SKM_GN.jsx
@@ -150,6 +150,11 @@ function MitoGraphicalAnalysisGastrocnemius() {
                   <img src={`${imageURL}/figure_7.png`} width="100%" alt="" />
                   <img src={`${imageURL}/figure_8.png`} width="100%" alt="" />
                 </p>
+                <DataVizLink
+                  title="timecourse"
+                  tissue="Gastrocnemius"
+                  plotType="Trajectories"
+                />
                 <hr />
               </div>
               <div className="section level4">
diff --git a/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/SKM_VL.jsx b/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/SKM_VL.jsx
index 9456a30b..ad9530b3 100644
--- a/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/SKM_VL.jsx
+++ b/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/SKM_VL.jsx
@@ -150,6 +150,11 @@ function MitoGraphicalAnalysisVastusLateralis() {
                   <img src={`${imageURL}/figure_7.png`} width="100%" alt="" />
                   <img src={`${imageURL}/figure_8.png`} width="100%" alt="" />
                 </p>
+                <DataVizLink
+                  title="timecourse"
+                  tissue="Vastus Lateralis"
+                  plotType="Trajectories"
+                />
                 <hr />
               </div>
               <div className="section level4">
diff --git a/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/SMLINT.jsx b/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/SMLINT.jsx
index edcf32b7..a918a66c 100644
--- a/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/SMLINT.jsx
+++ b/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/SMLINT.jsx
@@ -148,6 +148,11 @@ function MitoGraphicalAnalysisSmallIntestine() {
                   <img src={`${imageURL}/figure_7.png`} width="100%" alt="" />
                   <img src={`${imageURL}/figure_8.png`} width="100%" alt="" />
                 </p>
+                <DataVizLink
+                  title="timecourse"
+                  tissue="Small Intestine"
+                  plotType="Trajectories"
+                />
                 <hr />
               </div>
             </div>
diff --git a/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/SPLEEN.jsx b/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/SPLEEN.jsx
index 6f022bed..ff520971 100644
--- a/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/SPLEEN.jsx
+++ b/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/SPLEEN.jsx
@@ -147,6 +147,11 @@ function MitoGraphicalAnalysisSpleen() {
                   No significant enrichments for
                   SPLEEN:1w_F0_M0-&gt;2w_F0_M0-&gt;4w_F0_M0-&gt;8w_F1_M1
                 </p>
+                <DataVizLink
+                  title="timecourse"
+                  tissue="Spleen"
+                  plotType="Trajectories"
+                />
                 <hr />
               </div>
             </div>
diff --git a/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/WAT_SC.jsx b/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/WAT_SC.jsx
index 506d1578..e6bb7f55 100644
--- a/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/WAT_SC.jsx
+++ b/src/AnalysisPage/GraphicalClustering/Pass1bMitoTissues/WAT_SC.jsx
@@ -150,6 +150,11 @@ function MitoGraphicalAnalysisWhiteAdipose() {
                   <img src={`${imageURL}/figure_7.png`} width="100%" alt="" />
                   <img src={`${imageURL}/figure_8.png`} width="100%" alt="" />
                 </p>
+                <DataVizLink
+                  title="timecourse"
+                  tissue="White Adipose"
+                  plotType="Trajectories"
+                />
                 <hr />
               </div>
               <div className="section level4">

From 8b712bdc441ef9df100972f6b7226699da421046 Mon Sep 17 00:00:00 2001
From: Jimmy Zhen <jzhen@stanford.edu>
Date: Thu, 2 May 2024 19:58:14 -0700
Subject: [PATCH 5/5] Add announcement item for companion paper

---
 src/AnnouncementsPage/announcements.json | 29 ++++++++++++++++++++----
 1 file changed, 25 insertions(+), 4 deletions(-)

diff --git a/src/AnnouncementsPage/announcements.json b/src/AnnouncementsPage/announcements.json
index df5b06a4..557905ec 100644
--- a/src/AnnouncementsPage/announcements.json
+++ b/src/AnnouncementsPage/announcements.json
@@ -136,6 +136,27 @@
     {
         "aid": 7,
         "posted_date": "2024-05-01",
+        "title": "MoTrPAC gene regulation study published in Nature Communications",
+        "content": "This study integrated MoTrPAC multi-tissue differential gene expression results with external genetic, transcriptomic, and other data. Several computational approaches were leveraged to explore possible ways in which exercise may modulate complex trait variation, including disease severity and risk.",
+        "metadata": {
+            "target": "external",
+            "tags": [
+                "companion-paper-published"
+            ],
+            "icon": "auto_stories"
+        },
+        "links": [
+            {
+                "label": "The impact of exercise on gene regulation in association with complex trait genetics",
+                "url": "https://doi.org/10.1038/s41467-024-45966-w",
+                "gaEventCategory": "MoTrPAC Companion Paper",
+                "gaEventAction": "Nature Publication"
+            }
+        ]
+    },
+    {
+        "aid": 8,
+        "posted_date": "2024-05-01",
         "title": "MoTrPAC animal molecular adaptations study published in Cell Genomics",
         "content": "In an integrated analysis of DNA methylation, chromatin accessibility, and transcriptome in eight tissues from the control group, we identified distinct molecular landscapes across rat tissues. We demonstrated that the transcriptional and epigenetic responses to eight weeks of exercise training are predominantly tissue-specific and implicated GPCR-encoding genes as potential mediators of the molecular adaptations to training.",
         "metadata": {
@@ -155,7 +176,7 @@
         ]
     },
     {
-        "aid": 8,
+        "aid": 9,
         "posted_date": "2024-05-01",
         "title": "MoTrPAC animal physiological adaptations study published in Function",
         "content": "This paper extensively characterizes physiological adaptations to progressive endurance exercise in fully mature adult and aged rats, serving as a phenotypic compendium of the MoTrPAC pre-clinical animal endurance training data resource. Ultimately, the goal of this resource is to foster phenotypic and multi-omic data integration to develop an integrative molecular map of time-, sex-, and age-specific responses to endurance exercise training.",
@@ -176,7 +197,7 @@
         ]
     },
     {
-        "aid": 9,
+        "aid": 10,
         "posted_date": "2024-05-01",
         "title": "MoTrPAC animal white adipose tissue study published in Nature Metabolism",
         "content": "Multi-omic profiling identifies profound sexual dimorphism in the subcutaneous white adipose tissue (scWAT) molecular landscape of sedentary rats that is largely preserved or amplified with training.  Using a computational approach, we identify candidate molecular regulators of sexually dimorphic scWAT phenotypic responses to training, demonstrating the resource utility of MoTrPAC-generate data to drive novel hypothesis-based research in the field.",
@@ -197,7 +218,7 @@
         ]
     },
     {
-        "aid": 10,
+        "aid": 11,
         "posted_date": "2024-05-01",
         "title": "MoTrPAC animal endurance training study published in Nature",
         "content": "The main MoTrPAC animal endurance training study has been published in Nature. This study profiled the temporal transcriptome, proteome, metabolome, lipidome, phosphoproteome, acetylproteome, ubiquitylproteome, epigenome, and immunome in whole blood, plasma, and 18 solid tissues in male and female rats over 8 weeks of endurance exercise training. The resulting data compendium encompasses 9466 assays across 19 tissues, 25 molecular platforms, and 4 training time points in young adult male and female rats.",
@@ -224,7 +245,7 @@
         ]
     },
     {
-        "aid": 11,
+        "aid": 12,
         "posted_date": "2024-05-02",
         "title": "MoTrPAC mitochondrial response study published in Cell Metabolism",
         "content": "The MoTrPAC Mitochondria companion paper has been published in the Cell Metabolism. This study provides a multi-omic, cross-tissue atlas of the mitochondrial response to training and identify candidates for prevention of disease-associated mitochondrial dysfunction.",