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

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Wen Yang
Wen Yang 2020-10-30
评论： Wen Yang 2020-11-3
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.

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Scott Ronquist
Scott Ronquist 2020-11-2
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.
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Scott Ronquist
Scott Ronquist 2020-11-3
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)

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