[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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