The heatmap.2() function does not perform scaling of the data by default (unlike the base heatmap function). Thus your data has bright green bands because those rows have values in the upper range of your distribution and you've set high values to be green, while the black rows have values close to zero. The histogram in the key is telling you the frequency of values overall in the data set. You can see that the distribution has a right shoulder towards green. The trace down each column is telling you the size of the measurements by column position.
Why did you draw this heat map? What did you expect to see? Depending on your needs, you might choose to scale the data (see ?heatmap.2 ), or remove rows with little variation.