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image resize to points ... JOSS format
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ialbert committed Apr 2, 2024
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Expand Up @@ -76,7 +76,7 @@ GO:0005615,CC,1,extracellular space,C3P1,4,(1/4)

In the next step, GeneScape visualizes the GO terms as the graph structure that represents the functional context of the genes relative to the larger Gene Ontology.

![Ontology subgraph for a gene list \label{fig:interface}](images/genescape-output1.png){height="400px"}
![Ontology subgraph for a gene list \label{fig:interface}](images/genescape-output1.png){height="216pt"}

Various colors are used to provide additional context to the nodes in the graph; for example, functions derived from the input genes are colored green. The intermediate nodes are colored by their category.

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The filtering process will result in a smaller tree focused on the lipid-related terms:

![Filtering a large graph for a specific term \label{fig:filter}](images/genescape-output3.png){height="400px"}
![Filtering a large graph for a specific term \label{fig:filter}](images/genescape-output3.png){height="216pt"}

In addition, users can zoom in and out of the tree. The software's command-line version supports generating outputs in various formats, such as PDF or PNG.

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