PDF plots in gene-patterns.Rmd

[menoldmt]

Large PDF-saved gene-pattern plots are improperly zoomed in and facet label edges are cropped. This is evident when using dev.copy and dev.off here for saving plots, more so with larger ones due to more gene pattern clusters.

Expected Behavior:

• PDF plots should fully display facet labels without undue zooming or cropping, preserving
  appearance and layout irrespective of plot size.
   
  Proposed Solution:
• Replace dev.copy and dev.off lines with ggplot2::ggsave