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

Olivier Delalleau shish@keba...
Sat Sep 24 09:36:07 CDT 2011


I'm sorry I can't help on your questions, but maybe you should ask on
matplotlib-users instead (
https://lists.sourceforge.net/lists/listinfo/matplotlib-users).

-=- Olivier

2011/9/24 fdu.xiaojf@gmail.com <fdu.xiaojf@gmail.com>

> **
> 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.pngas 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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