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_... 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
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
** 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_... 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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participants (2)
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fdu.xiaojf@gmail.com
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Olivier Delalleau