VariantRecalibrator: Problem in R script

Hello,

I run variantRecalibrator command on vcf files. I got error message in R plot. I try to debug the generated R script from variantRecalibrator. I had all 3 library(ggplot2,tools,grid). As i have new R version, i have changed couple of things in the script. opts() changed to theme(), theme_rect to element_rect. I am still getting error.(Error in (function (el, elname) :). Do anyone have updated R script for new version of R and ggplot. I have attached my R script.

I will be glad to know list of changes need to make in R script.

Iam using R 3.1, Gatk 3.1.1.

Thanks

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