Pie charts are generally not a good way to represent data because they convey an information that the eye cannot judge correctly.

Quoting the R documentation for ?pie:

 Pie charts are a very bad way of displaying information.  The eye
 is good at judging linear measures and bad at judging relative
 areas.  A bar chart or dot chart is a preferable way of displaying
 this type of data.

 Cleveland (1985), page 264: “Data that can be shown by pie charts
 always can be shown by a dot chart.  This means that judgements of
 position along a common scale can be made instead of the less
 accurate angle judgements.” This statement is based on the
 empirical investigations of Cleveland and McGill as well as
 investigations by perceptual psychologists.

[...]

 Cleveland, W. S. (1985) _The elements of graphing data_.
 Wadsworth: Monterey, CA, USA.

Here is a quick example from Wikipedia of how bad our eye can distinguish this type of information:

.

So I would go either for a barchart representation of the blast2go output, or for a network representation such as the one provided by topGO.