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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 / heat map heatmap task node to launch the heat mapheatmap
The Dendrogram view will open showing a heat map heatmap 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.
The heat map heatmap displays standardized expression values with a mean of zero and standard deviation of one.
The heat map heatmap can be customized to improve data visualization using the menu on the Configuration panel on the left.
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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 heatmap as a publication-quality image.
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- Select Save
The heat map heatmap will be saved as a .svg file and downloaded in your web browser.
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