Hello all,
I am having problems with visualizing especially small genic regions in GenVisR. I am visualizing copy number segmentation data. GenVisR is an R package that uses ggplot2 to create visualizations of copy number gain/loss data. Specifically, I am using the cnFreq() function to create a copy number plot for a cohort of samples, which displays copy number gain/loss proportions over the entire genome. However, I cannot get all valid copy number proportions to show. I have about 50% of my samples with a copy number loss on chr7 in a pretty limited genic range (say maybe 2000bp), but the final view shows only 25%. When zooming in on just chr7, the 2kb spike suddenly appears at 50%. This tells me that the data is properly calculated, but there is some limitation with how GenVisR is implementing ggplot2 to visualize the data. GenVisR's implementation can be found here. I am new to ggplot2, but I suspect that I need a way to force visualization of very small regions. Is there a way to normalize these small regions for this purpose? Or maybe is there a way to say "any segments below this size, display as this larger size". Thanks.
-JCN
