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Connects to #343. Connects to #346. Modified graphical clustering pathway enrichment description text. Updated Data Hub tutorial video source. #347

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merged 10 commits into from
Jun 2, 2024
Merged

Connects to #343. Connects to #346. Modified graphical clustering pathway enrichment description text. Updated Data Hub tutorial video source. #347

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9c50e9f
Add youtube player dependency
jimmyzhen May 25, 2024
74b2d1c
Replace tutorial video hosted on Google Drive with embedded youtube v…
jimmyzhen May 25, 2024
9ba4183
Delete unused image import
jimmyzhen May 25, 2024
5f6d2be
Update bullet point text
jimmyzhen May 30, 2024
e50e342
Add styling to MAWG resources section tabs
jimmyzhen May 30, 2024
a6d302e
New component to render pathway network description common to all gra…
jimmyzhen Jun 2, 2024
d8ea00b
Replace embedeed pathway network description text with component
jimmyzhen Jun 2, 2024
ba479bf
Replace embedded pathway network description text with component
jimmyzhen Jun 2, 2024
e4e4bbd
Fix component's prop definition
jimmyzhen Jun 2, 2024
3d09e4c
Dependency versions changed due to yarn install
jimmyzhen Jun 2, 2024
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1 change: 1 addition & 0 deletions package.json
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@
"react-scripts": "5.0.1",
"react-table": "^7.7.0",
"react-tooltip": "^5.11.2",
"react-youtube": "^10.1.0",
"redux": "^4.0.1",
"redux-thunk": "^2.3.0",
"tocbot": "^4.25.0",
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62 changes: 5 additions & 57 deletions src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/ADRNL.jsx
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@ import {
pass1b06GraphicalClusteringLandscapeImageLocation,
} from '../sharedLib';
import DataVizLink from '../components/dataVizLink';
import PathwayNetworkDescription from '../components/pathwayNetworkDescription';

function GraphicalAnalysisAdrenal() {
// initialize table of contents
Expand Down Expand Up @@ -83,63 +84,10 @@ function GraphicalAnalysisAdrenal() {
</div>
</div>
<div className="section level2">
<h2 id="detailed-view-of-selected-clusters">
Detailed view of selected clusters
</h2>
<p>
Here we show highlighted trees, top pathway enrichments, network
view of <em>all</em> pathway enrichments, and sample-level
trajectories for each selected cluster (node, edge, or path).
</p>
<p>
<strong>Interactive networks of pathway enrichments</strong>
</p>
<p>
These networks summarize all significant pathway enrichments for a
set of differential analytes. Results from all omes are combined.
</p>
<p>
Each node is a pathway. Hover over a node to see the pathway name
(and parent pathway in parentheses), nominal enrichment p-value,
datasets in which this pathway was significantly enriched, and the
union of genes at the intersection of the input features and
pathway members. Larger nodes indicate that more datasets (e.g.
METAB;SKM-GN) were significantly enriched for this pathway.{' '}
<strong>
Pathways only enriched with metabolites are not shown because
edges are defined using genes, not KEGG IDs.
</strong>
</p>
<p>
Edges are drawn between nodes if there is a substantial overlap in
the intersection of the input features and pathway members for
both pathways. Hover over an edge to see the similarity score and
list of genes in the intersection.
</p>
<p>
Nodes are colored to visually separate groups of related pathway
enrichments. Each group has a label (rectangular node), which
corresponds to the most frequently occurring parent pathway in the
group. These labels are meant to help summarize groups of related
pathway enrichments.
</p>
<p>Explore these interactive plots!</p>
<ul>
<li>
Hover over nodes (pathways) and edges (intersection between
pathways) to see more information
<br />
</li>
<li>
Click nodes to highlight them and connected edges
<br />
</li>
<li>
Zoom in and out
<br />
</li>
<li>Click and drag nodes</li>
</ul>
<PathwayNetworkDescription
tissue="Adrenal"
clusterName="1w_F-1_M1-&gt;2w_F-1_M0-&gt;4w_F-1_M0-&gt;8w_F-1_M0"
/>

<div className="section level3">
<h3 id="selected-paths">Selected paths</h3>
Expand Down
62 changes: 5 additions & 57 deletions src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/BAT.jsx
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@ import {
pass1b06GraphicalClusteringLandscapeImageLocation,
} from '../sharedLib';
import DataVizLink from '../components/dataVizLink';
import PathwayNetworkDescription from '../components/pathwayNetworkDescription';

function GraphicalAnalysisBrownAdipose() {
// initialize table of contents
Expand Down Expand Up @@ -84,63 +85,10 @@ function GraphicalAnalysisBrownAdipose() {
</div>
</div>
<div className="section level2">
<h2 id="detailed-view-of-selected-clusters">
Detailed view of selected clusters
</h2>
<p>
Here we show highlighted trees, top pathway enrichments, network
view of <em>all</em> pathway enrichments, and sample-level
trajectories for each selected cluster (node, edge, or path).
</p>
<p>
<strong>Interactive networks of pathway enrichments</strong>
</p>
<p>
These networks summarize all significant pathway enrichments for a
set of differential analytes. Results from all omes are combined.
</p>
<p>
Each node is a pathway. Hover over a node to see the pathway name
(and parent pathway in parentheses), nominal enrichment p-value,
datasets in which this pathway was significantly enriched, and the
union of genes at the intersection of the input features and
pathway members. Larger nodes indicate that more datasets (e.g.
METAB;SKM-GN) were significantly enriched for this pathway.{' '}
<strong>
Pathways only enriched with metabolites are not shown because
edges are defined using genes, not KEGG IDs.
</strong>
</p>
<p>
Edges are drawn between nodes if there is a substantial overlap in
the intersection of the input features and pathway members for
both pathways. Hover over an edge to see the similarity score and
list of genes in the intersection.
</p>
<p>
Nodes are colored to visually separate groups of related pathway
enrichments. Each group has a label (rectangular node), which
corresponds to the most frequently occurring parent pathway in the
group. These labels are meant to help summarize groups of related
pathway enrichments.
</p>
<p>Explore these interactive plots!</p>
<ul>
<li>
Hover over nodes (pathways) and edges (intersection between
pathways) to see more information
<br />
</li>
<li>
Click nodes to highlight them and connected edges
<br />
</li>
<li>
Zoom in and out
<br />
</li>
<li>Click and drag nodes</li>
</ul>
<PathwayNetworkDescription
tissue="Brown Adipose"
clusterName="1w_F-1_M0-&gt;2w_F-1_M0-&gt;4w_F-1_M0-&gt;8w_F0_M1"
/>

<div className="section level3">
<h3 id="selected-paths">Selected paths</h3>
Expand Down
62 changes: 5 additions & 57 deletions src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/BLOOD.jsx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@ import {
pass1b06GraphicalClusteringLandscapeImageLocation,
} from '../sharedLib';
import DataVizLink from '../components/dataVizLink';
import PathwayNetworkDescription from '../components/pathwayNetworkDescription';

function GraphicalAnalysisBlood() {
// initialize table of contents
Expand Down Expand Up @@ -79,63 +80,10 @@ function GraphicalAnalysisBlood() {
</div>
</div>
<div className="section level2">
<h2 id="detailed-view-of-selected-clusters">
Detailed view of selected clusters
</h2>
<p>
Here we show highlighted trees, top pathway enrichments, network
view of <em>all</em> pathway enrichments, and sample-level
trajectories for each selected cluster (node, edge, or path).
</p>
<p>
<strong>Interactive networks of pathway enrichments</strong>
</p>
<p>
These networks summarize all significant pathway enrichments for a
set of differential analytes. Results from all omes are combined.
</p>
<p>
Each node is a pathway. Hover over a node to see the pathway name
(and parent pathway in parentheses), nominal enrichment p-value,
datasets in which this pathway was significantly enriched, and the
union of genes at the intersection of the input features and
pathway members. Larger nodes indicate that more datasets (e.g.
METAB;SKM-GN) were significantly enriched for this pathway.{' '}
<strong>
Pathways only enriched with metabolites are not shown because
edges are defined using genes, not KEGG IDs.
</strong>
</p>
<p>
Edges are drawn between nodes if there is a substantial overlap in
the intersection of the input features and pathway members for
both pathways. Hover over an edge to see the similarity score and
list of genes in the intersection.
</p>
<p>
Nodes are colored to visually separate groups of related pathway
enrichments. Each group has a label (rectangular node), which
corresponds to the most frequently occurring parent pathway in the
group. These labels are meant to help summarize groups of related
pathway enrichments.
</p>
<p>Explore these interactive plots!</p>
<ul>
<li>
Hover over nodes (pathways) and edges (intersection between
pathways) to see more information
<br />
</li>
<li>
Click nodes to highlight them and connected edges
<br />
</li>
<li>
Zoom in and out
<br />
</li>
<li>Click and drag nodes</li>
</ul>
<PathwayNetworkDescription
tissue="Blood RNA"
clusterName="1w_F0_M1-&gt;2w_F0_M1-&gt;4w_F0_M1-&gt;8w_F1_M1"
/>
<div className="section level3">
<h3 id="selected-paths">Selected paths</h3>
<div className="section level4">
Expand Down
62 changes: 5 additions & 57 deletions src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/COLON.jsx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@ import {
pass1b06GraphicalClusteringLandscapeImageLocation,
} from '../sharedLib';
import DataVizLink from '../components/dataVizLink';
import PathwayNetworkDescription from '../components/pathwayNetworkDescription';

function GraphicalAnalysisColon() {
// initialize table of contents
Expand Down Expand Up @@ -79,63 +80,10 @@ function GraphicalAnalysisColon() {
</div>
</div>
<div className="section level2">
<h2 id="detailed-view-of-selected-clusters">
Detailed view of selected clusters
</h2>
<p>
Here we show highlighted trees, top pathway enrichments, network
view of <em>all</em> pathway enrichments, and sample-level
trajectories for each selected cluster (node, edge, or path).
</p>
<p>
<strong>Interactive networks of pathway enrichments</strong>
</p>
<p>
These networks summarize all significant pathway enrichments for a
set of differential analytes. Results from all omes are combined.
</p>
<p>
Each node is a pathway. Hover over a node to see the pathway name
(and parent pathway in parentheses), nominal enrichment p-value,
datasets in which this pathway was significantly enriched, and the
union of genes at the intersection of the input features and
pathway members. Larger nodes indicate that more datasets (e.g.
METAB;SKM-GN) were significantly enriched for this pathway.{' '}
<strong>
Pathways only enriched with metabolites are not shown because
edges are defined using genes, not KEGG IDs.
</strong>
</p>
<p>
Edges are drawn between nodes if there is a substantial overlap in
the intersection of the input features and pathway members for
both pathways. Hover over an edge to see the similarity score and
list of genes in the intersection.
</p>
<p>
Nodes are colored to visually separate groups of related pathway
enrichments. Each group has a label (rectangular node), which
corresponds to the most frequently occurring parent pathway in the
group. These labels are meant to help summarize groups of related
pathway enrichments.
</p>
<p>Explore these interactive plots!</p>
<ul>
<li>
Hover over nodes (pathways) and edges (intersection between
pathways) to see more information
<br />
</li>
<li>
Click nodes to highlight them and connected edges
<br />
</li>
<li>
Zoom in and out
<br />
</li>
<li>Click and drag nodes</li>
</ul>
<PathwayNetworkDescription
tissue="Colon"
clusterName="1w_F0_M0-&gt;2w_F0_M0-&gt;4w_F0_M0-&gt;8w_F1_M1"
/>

<div className="section level3">
<h3 id="selected-paths">Selected paths</h3>
Expand Down
59 changes: 2 additions & 57 deletions src/AnalysisPage/GraphicalClustering/Pass1bLandscapeTissues/CORTEX.jsx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@ import {
pass1b06GraphicalClusteringLandscapeImageLocation,
} from '../sharedLib';
import DataVizLink from '../components/dataVizLink';
import PathwayNetworkDescription from '../components/pathwayNetworkDescription';

function GraphicalAnalysisCortex() {
// initialize table of contents
Expand Down Expand Up @@ -80,63 +81,7 @@ function GraphicalAnalysisCortex() {
</div>
</div>
<div className="section level2">
<h2 id="detailed-view-of-selected-clusters">
Detailed view of selected clusters
</h2>
<p>
Here we show highlighted trees, top pathway enrichments, network
view of <em>all</em> pathway enrichments, and sample-level
trajectories for each selected cluster (node, edge, or path).
</p>
<p>
<strong>Interactive networks of pathway enrichments</strong>
</p>
<p>
These networks summarize all significant pathway enrichments for a
set of differential analytes. Results from all omes are combined.
</p>
<p>
Each node is a pathway. Hover over a node to see the pathway name
(and parent pathway in parentheses), nominal enrichment p-value,
datasets in which this pathway was significantly enriched, and the
union of genes at the intersection of the input features and
pathway members. Larger nodes indicate that more datasets (e.g.
METAB;SKM-GN) were significantly enriched for this pathway.{' '}
<strong>
Pathways only enriched with metabolites are not shown because
edges are defined using genes, not KEGG IDs.
</strong>
</p>
<p>
Edges are drawn between nodes if there is a substantial overlap in
the intersection of the input features and pathway members for
both pathways. Hover over an edge to see the similarity score and
list of genes in the intersection.
</p>
<p>
Nodes are colored to visually separate groups of related pathway
enrichments. Each group has a label (rectangular node), which
corresponds to the most frequently occurring parent pathway in the
group. These labels are meant to help summarize groups of related
pathway enrichments.
</p>
<p>Explore these interactive plots!</p>
<ul>
<li>
Hover over nodes (pathways) and edges (intersection between
pathways) to see more information
<br />
</li>
<li>
Click nodes to highlight them and connected edges
<br />
</li>
<li>
Zoom in and out
<br />
</li>
<li>Click and drag nodes</li>
</ul>
<PathwayNetworkDescription />

<div className="section level3">
<h3 id="selected-paths">Selected paths</h3>
Expand Down
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