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The Hierarchical clustering menu will open (Figure 2).
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- Click Finish to run with default settings
A Hierarchical clustering task node will be added to the pipeline (Figure 3).
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- Double-click the Hierarchical clustering clustering / heat map task node to launch the heat map
The Dendrogram view will open showing a heat map with the hierarchical clustering results (Figure 4).
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Samples are shown on rows and genes on columns. Clustering for samples and genes is shown through the dendrogram trees. More similar samples/genes are separated by fewer branch points of the dendrogram tree.
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The heat map can be customized to improve data visualization using the menu on the left- Configuration panel on the left.
- Expand the Annotations > Data card.
- Click on the gray button on the right hand side of
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- Select 5-AZA Dose from the Attributes drop-down menuRow annot None available
- In the dialog, click on the Gene counts node
- Now set the Row annot to 5-AZA Doze
Samples are now labeled with their Treatment 5-AZA Doze group (Figure 5).
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Samples cluster based on treatment group and the 5μM and 10μM groups are more similar to each other than to the 0μM group.
We can save the heat map as a publication-quality image.
- Click Click the Save image icon in the top right corner of the plot
- Choose size and resolution using the Save as SVG dialog (Figure 6)
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- Select Save
The heat map will be saved as a .svg file and downloaded in your web browser.
For more information about hierarchical clustering and the Dendrogram view, please see the Hierarchical Clustering (Old Version) user guide.
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