Using "Pearson correlation coefficient" in the 'Pdist' for the Clustergram function

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I am doing the Hierarchical cluster analysis. I constructed the dendrograms by the 'clustergram' using agglomerative average-linkage clustering. But I need to use 'pearson correlation coeffiecient' for the distance matric(the default distance matric is euclidean, there are other matric availdable as well), but I could not find the pearson correlation available in the 'PDist' function. Thanks for helping.

Accepted Answer

Scott Ronquist
Scott Ronquist on 2 Nov 2020
The 'correlation' option for pdist uses the pearson correlation (documentation page here). So to use this metric to calculate the distance between columns in clustergram, you can call:
clustergram(..., "ColumnPDist", "correlation")
The same option is available for "RowPDist" as well.
  5 Comments
Scott Ronquist
Scott Ronquist on 3 Nov 2020
The apostrophe is used to transpose the matrix X.
corr calculates the correlation between the columns of the input matrix. pdist calculates the distance between the rows of the input matrix. The apostrophe operator computes the complex conjugate transpose of X. When the values of X are all real numbers (as is the case here), this is the same as the basic transpose function.
X' can be replaced with transpose(X) in the code from above:
X = rand(5,2);
pdist(transpose(X), "correlation")
1-corr(X)
Wen Yang
Wen Yang on 3 Nov 2020
The penny dropped. Thank you so much Ronquist for your help, patient and hardworking.

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