Can i change the colors background axes etc of the plots in weka

Sure, this information is stored in the Visualize.props properties file:

  • weka.gui.visualize.Plot2D.axisColour defines the color of the axes
  • weka.gui.visualize.Plot2D.backgroundColour sets the background color

For more information see the articles about properties file (especially the section Precedence will tell you where to place the .props file.) and Visualize.props itself.