The Heat Map is a color-coded hierarchical cluster analysis that displays individual values in the results of a cluster analysis of a data matrix. The cluster analysis groups rows and columns that have similar abundance values to each other. You can use the heat map to cluster abundance values of proteins and peptides.

You can select from the options to give visual clarity or prominence to what is important in the results.

Procedure

  1. Open the result file, and select the Proteins tab.
  2. Select Distribution Charts .
  3. Select the Heat Map tab.
  4. The Heat Map opens.
  5. Sample heat map
  6. At the left and the top of the heat map, dendrograms display the cluster nodes of the cluster analysis of rows and columns. The size of the dendrograms visualize the similarity between two cluster nodes, the closer two nodes are, the more similar.
  7. The dendogram above the heat map represents the distance (or similarity) between samples. The height of each node is proportional to the distances (or similarity) between two samples at the lowest level or two sample clusters at the higher levels.
  8. Pointing to a dendogram node displays the distance between clusters.
  9. Pointing to a heat map cell displays the compound and sample information.
  10. You can zoom in by drawing a zoom rectangle on the heat map. You can also zoom using the dendrogram:
  11. Hold the cursor over a dendrogram. A green rectangle highlights the cluster tree under the cursor.
  12. Double-click when the cluster node of interest is highlighted.
  13. You can zoom out of the heat map using the arrow icons at the top of the dendrograms or by right-click the heat map and choosing the associated entry in the context menu. You can zoom out incrementally, or choose an undo all zoom.
  14. On the left side panel of the Heat Map page, For Color By, select one or all.
  15. (Optional) For Filter By, select one or all settings.
  16. Under Other Settings, make selections in Column Settings and in Row Settings for displaying clusters or labels.
  17. See Heat Map Parameters for a description of the parameters.
  18. (Optional) For Color Scheme, choose a color scheme.
  19. This option is also available by right-clicking in the UI.
  20. For Distance Function, choose the appropriate selection.
  21. See Heat Map Parameters for a description of the parameters.
  22. Linkage Method, choose the appropriate selection.
  23. See Heat Map Parameters for a description of the parameters.
  24. For X-Axis Label, choose the information to display on the X-axis.
  25. This setting requires selecting Column Settings Show Labels.
  26. In the results file, filter the result table to use as a data source.
  27. Make the selections for Scale Before Clustering.
  28. Select Refresh button to update the clustering.
  29. The cluster results are displayed afterwards. The button is highlighted when the results are not current.