Hello! Iunderstand that CNVkit plots the heatmap ordering the samples alphabetically or following a provided order; but, I need to make a clustering for the samples. I need to plot them according to a mathematical order to see which samples are similar or different regarding Log2 value. I want to know if it's possible to do that with CNVkit and how to do it. If not, I would like to know how to order the data to plot it with another tool. Thanks a lot!
CNVkit plots the samples in the order that you list the .cns files on the command. It doesn't do hierarchical clustering on its own, but if you use R or another program to e.g. hierarchically cluster the log2 values in the .cnr files, then you can observe the sample ordering there and reuse that ordering when you run
cnvkit.py heatmap to get the same order.