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The Hierarchical clustering menu will open (Figure 2). Hierarchical clustering can be performed with a heatmap or bubble map plot. Cluster must be selected under Ordering for both Feature order and Cell order if both the features (columns) and cells (rows) are to be clustered. 

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• Click Finish to run with default settings

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• Double-click the Hierarchical clustering / heatmap task node to launch the heatmap

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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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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 heatmap as a publication-quality image. 

• Click the Save Export image icon Image Removed Image Addedin the top right corner of the plot
• Choose size and resolution using the Save as SVG dialog (Figure 6)
  
  

• Select Save

The heatmap 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  user guide. 

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