[Numpy-discussion] How to plot heatmap in matplotlib?

fdu.xiaojf at gmail.com fdu.xiaojf at gmail.com
Sat Sep 24 00:24:28 EDT 2011

  Dear all,

Heatmap (like those on the page 
is a frequently used type of image in microarray data analysis. However, 
it seems there are no convenient functions in matplotlib to plot heatmap 
(please correct me if I was wrong), so I'm planning to write my own.

Let me take the heatmap by the link 
as an example, which is produced by R.

With my limited knowledge and expertise of matplotlib, I have the 
following questions and I hope you guys could help me.

1) I tend to use pcolor to draw the colormap in the central area. 
However, I've seen a lot of examples draw colormap with imshow.

    What's the difference between pcolor and imshow?
    Shall I use pcolor or imshow to produce the heatmap in the link above?

2) How to draw the dendrograms on the top and left of the colormap?

    I got hints from 
on how to append axes to current plot, but I still have now idea how to 
draw the dengrograms.

3) How to draw the column side colormap (the smaller one) between the 
top dendrogram and the big colormap?

4) I can use colorbar to draw a colorbar, but how to place the colorbar 
on the topleft of the image just as the R heatmap does?

5) Any other suggestions on how to draw the heatmap?

Thanks and any help will be greatly appreciated.


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