Grey zone in dendrogram (heatmap) after filtering

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When applying variable and sample filters to a dendrogram, the cells being filtered out are not deleted, instead, they are grey out. The reason is that, in dendrogram, we have to keep the grey cells to maintain the original tree structure from the clustering analysis.


There are two ways to remove grey zone:

1. Filter the variables/observations first and do the clustering again on the remaining data. The clustering results will not in the same order as the old one since the input data is changed.

20130611 RemoveDendrogramGrey 1.png


2. Record the tree structure by saving sample and variable lists, and then regenerate a heatmap with the saved lists.

  • Click on the "Generate Observation List" and "Generate Variable List" options in the Task tab of View Controller (usually on right bottom).
  • Reorder the whole Omic Data by these two lists using OmicData | Subset function.
  • Click on the new Omic Data and add a HeatMap View, which will be the same as the clustering results but missing the dendrogram tree.