[SciPy-User] Color Lists in Dendrograms / Hierarchical Clustering

[Daniel Miner]

Hi everyone,

I'd written over a month ago but never got any replies, so I'm trying again. Any help would be sincerely appreciated.

I'm trying to use hierarchical clustering to tease out some structure in data that I already know exists as a sort of test case to (hopefully) show that it can be reliably done for the type of data I'm concerned with. To this end, knowing that the full call for dendrogram generation is:

scipy.cluster.hioerarchy.dendrogram(Z, p=30, truncate_mode=None, color_threshold=None, get_leaves=True, orientation='top',labels=None, count_sort=False, distance_sort=False, show_leaf_counts=True, no_plot=False, no_labels=False, color_list=None,leaf_font_size=None, leaf_rotation=None, leaf_label_func=None, no_leaves=False, show_contracted=False,link_color_func=None)

I use one of the linkage algorithms to generate the linkage, manually create a list of colors "c_list" as a list with a color corresponding to each known category of original data for each data point - i.e. if I have data [1,2,3] and know that 1 and 2 come from the same category but 3 is different, I make a list ['r','r','g'] - and try to use it as follows:

import matplotlib.pyplot as pt
import scipy.cluster.hierarchy as sc
[import other stuff]
[load data DAT, generate color list]
lw = sc.ward(DAT)
dw = sc.dendrogram(lw,color_list='c_list')
pt.show()

However, the colors seem to do nothing. I've tried listing them both numerically (i.e. [1,2,3]) and as characters (i.e. ['r','g','b']), and have tried making the call with c_list in single quotes as shown and with no quotes at all. There is no documentation at http://docs.scipy.org/doc/scipy/reference/generated/scipy.cluster.hierarchy.dendrogram.html regarding an expected format for the color list, and without this color labeling, I can't check to see if the clustering is doing what I hope it does, as there are many data points and it would be prohibitively difficult to read though each of the tiny index labels at the bottom of the default dendrogram plot. I really have no idea how to proceed in order to make this work and am hoping that someone here can provide some advice. Thanks.

Best regards,
Daniel
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