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