Black line in the following graph is plotting using the below command for matplotlib python
pylab.semilogy(xaxis, pq_averages, \'ks-\',color=\'black\', label=\'D
Try adding markerfacecolor like so:
markerfacecolor
pylab.semilogy(xaxis, pq_averages, 'ks-', markerfacecolor='none', label='DCTCP-PQ47.5')