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

fdu.xiaojf@gmai... fdu.xiaojf@gmai...
Fri Sep 23 23:24:28 CDT 2011


  Dear all,

Heatmap (like those on the page 
http://www2.warwick.ac.uk/fac/sci/moac/students/peter_cock/r/heatmap/) 
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 
http://www2.warwick.ac.uk/fac/sci/moac/students/peter_cock/r/heatmap/scaled_color_key.png 
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 
http://matplotlib.sourceforge.net/examples/axes_grid/scatter_hist.html 
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.

Regards,
Jianfeng





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