Graph characteristics
++ Graphical analysis has replaced clustering as the primary method + of exploring main patterns in the PASS1B data. This approach is + more flexible and gives us better resolution. +
+All paths
+Tree of ALL differential analytes (all paths)
+ +
+ 
+
Top clusters
++ A “cluster” is a path, node, or edge. Here we show the size and + ome distributions for selected clusters in this tissue. +
+ +
+ 
+
Top 5 trajectories
++ Here we show trees of the 5 largest trajectories (also called + paths) in this tissue, either with all differential features or + features split by ome group. +
+All omes
+ +
+ 
+
Split by ome group
+ +
+ 
+
+ Detailed view of selected clusters +
++ Here we show highlighted trees, top pathway enrichments, network + view of all pathway enrichments, and sample-level + trajectories for each selected cluster (node, edge, or path). +
++ Interactive networks of pathway enrichments +
++ These networks summarize all significant pathway enrichments for a + set of differential analytes. Results from all omes are combined. +
++ 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.{' '} + + Pathways only enriched with metabolites are not shown because + edges are defined using genes, not KEGG IDs. + +
++ 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. +
++ 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. +
+Explore these interactive plots!
+-
+
-
+ Hover over nodes (pathways) and edges (intersection between
+ pathways) to see more information
+
+
+ -
+ Click nodes to highlight them and connected edges
+
+
+ -
+ Zoom in and out
+
+
+ - Click and drag nodes +
Selected paths
+ ++ ADRNL:1w_F-1_M1->2w_F-1_M0->4w_F-1_M0->8w_F-1_M0 +
+
+ 
+ 
+ 
+
+
+ ADRNL:1w_F1_M-1->2w_F1_M0->4w_F1_M0->8w_F1_M0 +
+
+ 
+ 
+ 
+
+
+ ADRNL:1w_F0_M-1->2w_F1_M0->4w_F1_M0->8w_F1_M0 +
+
+ 
+ 
+ 
+
+
+ ADRNL:1w_F0_M0->2w_F0_M0->4w_F0_M0->8w_F0_M1 +
+
+ 
+ 
+ 
+
+
+ ADRNL:1w_F0_M-1->2w_F0_M-1->4w_F0_M0->8w_F1_M0 +
+
+ 
+ 
+ 
+
+
Selected nodes
+ +ADRNL:4w_F-1_M0
+
+ 
+ 
+ 
+
+
ADRNL:2w_F-1_M0
+
+ 
+ 
+ 
+
+
ADRNL:8w_F-1_M-1
+
+ 
+ 
+ 
+
+
ADRNL:8w_F-1_M0
+
+ 
+ 
+ 
+
+
ADRNL:8w_F-1_M1
+
+ 
+ 
+ 
+
+
ADRNL:8w_F0_M-1
+
+ 
+ 
+ 
+
+
ADRNL:8w_F0_M1
+
+ 
+ 
+ 
+
+
ADRNL:8w_F1_M0
+
+ 
+ 
+ 
+
+
ADRNL:8w_F1_M1
+
+ 
+ 
+ 
+
+
Selected edges
+ +ADRNL:2w_F-1_M0—4w_F-1_M0
+
+ 
+ 
+ 
+
+
ADRNL:4w_F-1_M0—8w_F-1_M0
+
+ 
+ 
+ 
+
+
+ 
+ 
-```
-
-#### Using Open Iconic's SVG Sprite
-
-Open Iconic also comes in a SVG sprite which allows you to display all the icons in the set with a single request. It's like an icon font, without being a hack.
-
-Adding an icon from an SVG sprite is a little different than what you're used to, but it's still a piece of cake. *Tip: To make your icons easily style able, we suggest adding a general class to the* `