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Clustergram. Changing the range of the colorbar

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From a 17x17 array, I've plotted the attached clustergram. The array values range from 1 to 5. The values on the diagonal are equal to 1.
I have the following questions:
  1. The colorbar values are obviously wrong. They range from -3 to 3. The correct range should should be 1 to 5. There no negative values in the array. I tried colormapeditor but failed to find an answer to this problem.
  2. Is there a way to change the colours of the clustergram to correspond to the colorbar (say "parula")?
  6 Comments
Adam Danz
Adam Danz on 3 May 2021
Edited: Adam Danz on 3 May 2021
You're missing the line that reads in the table. What is rmsd? When i read in the table using readtable('rmsd.xls') the table cannot be converted to an array.
George
George on 3 May 2021
Thank you Adam.
rmsd.xls was imported into the workspace (rmsd) (17x17 table).
Then it was converted to double: rd = table2array(rmsd);
>> size(rd)
ans =
17 17
>> class(rd)
ans =
'double'
The rest of the code that I used to generate the heatmap/clustergram is as per my email of May 1, 2021

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Accepted Answer

Adam Danz
Adam Danz on 3 May 2021
Edited: Adam Danz on 3 May 2021
The color scale is based on standardized values even if standardize is set to none.
You can set the range of standardized values as a scalar using,
cgo_all = clustergram(rd,___);
cgo_all.DisplayRange = ____
which adjusts the range of the colorbar but will still contain negative values because of standardization.
It may be helpful to review this example from the documentation that explains that the data are standardized so that the mean is 0 which is why colorbar values are +/-.
Also see this coursera course that covers Matlab's Clustergram function.
  2 Comments
George
George on 3 May 2021
Many thanks once again.
You're absolutely right. I tweeked setting the 'Standardize' flag to 'none'. The diagonal in this case is zero which coincides with the white colour in the colorbar.

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