Clustergram. Changing the range of the colorbar

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")?

[DGM]

For most plots, you can set the colormap scaling with caxis(). That said, I'm not familiar with the type of plot you're generating or if that even applies in this case.

[George]

Thank you for the answers. I should clarify. The figure was generated with "clustergram" from the bioinformatics toolbox

https://www.mathworks.com/help/bioinfo/ref/clustergram.html?searchHighlight=clustergram&s_tid=srchtitle

Following the generation of the heatmap/dendrogram, the colorbar was generated from the live editor. My efforts to change the range (-3 to +3) to 1 to +5 failed. Trying to set colorbar by using "colorbar" in the command window overides the current heatmap/dendrogram and generates a new empty window with the colorbar.

[Adam Danz]

Please provide a minimal working example that we can copy-paste to instantly reproduce the problem. That will greatly reduce the time it takes to trouble shoot and reduce the amount of guess work.

[George]

Thanks a lot for the promt answer. I'm attaching the datafile (rmsd.xls).

I imported this data and used:

rd = table2array(rmsd);

OBPs ={'3n7h'; '3q8i'; '3v2l'; '3k13'; '60ii'; '3ogn'; '2gte'; '6hhe'; '3bjh'; '3r72'; '1dqe'; '2wc5'; '6jpm'; '4inw'; '4pt1'; '6qq4'; '5dic'} ### as labels

cgo_all = clustergram(rd,'Colormap',redbluecmap,'Standardize','Row')

set(cgo_all,'RowLabels',OBPs(1:17),'ColumnLabels',OBPs)

Thanks again for looking into this

[Adam Danz]

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]

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

Answer 1

[Adam Danz]

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.

[George]

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.

[George]

Accepted