Hello all,

I've posted the question in Stackoverflow but I thought I might get more responses here.

I was able to load my csv file into a numpy array:

    data = np.genfromtxt('csv_file', dtype=None, delimiter=',')
    
Now I would like to generate a heatmap.

I have 19 categories from 11 samples, along these lines:

	  COG                 station1        station2        station3          station4      
		COG0001        0.019393497    0.183122497    0.089911227    0.283250444    0.074110521
		COG0002        0.044632051    0.019118032    0.034625785    0.069892277    0.034073709
		COG0003            0.033066112         0            0           0             0
		COG0004        0.115086472    0.098805295    0.148167492    0.040019101    0.043982814
		COG0005        0.064613057    0.03924007    0.105262559    0.076839235    0.031070155    
		COG0006        0.079920475    0.188586049    0.123607421    0.27101229    0.274806929    
		COG0007        0.051727492    0.066311584    0.080655401    0.027024185    0.059156417        
		COG0008        0.126254841    0.108478559    0.139106704    0.056430812    0.099823028

I wanted to use matplotlib colormesh.

all the examples I could find used random number arrays.

I can get the plot easily with random numbers, however I can't get my csv file to plot. first it refuses to reshape. I have NaNs there so I tried masking but that failed too. Also, I had to delete the header and first column, is there a way to leave them and get labels for the axes? I've edited the original question to include an excerpt of the csv file.

any help and insights would be greatly appreciated.

many thanks
Here's a nickel, kid, go get yourself a better plotting library

	> library(ggplot2)
	> foo = read.table('foo.txt', header=T)
	> foomelt = melt(foo)
	Using COG as id variables
	> ggplot(foomelt, aes(x=COG, y=variable, fill=value)) + geom_tile() + scale_fill_gradient(low='white', high='steelblue')
	> ggsave('biostar.png')
	Saving 7.97" x 7.75" image


ggplot2 is plotting heaven and *way* better than matplotlib.  Use rpy2 to run from python - they even have ggplot2 examples in the docs.

![](https://imgur.com/fGTZT.png)