I created a jqPlot on the east pane. And I change the size of the pane to allow enough space for the chart. However, seems some part of the layout did not get refreshed at all. How do I notify the rest of the layout and make it refresh? Thanks in advance.

Simply use sizePane to let your layout know you just resized it.
Here is where the original answer coming from https://groups.google.com/forum/?fromgroups#!topic/jquery-ui-layout/u6BsKaArFNY