Good code example: https://www.r-bloggers.com/making-back-to-back-histograms/
Explanation as to why base plot should be saved as a separate object and referenced in subsequent plots: https://www.r-bloggers.com/adding-lines-or-points-to-an-existing-barplot/
Modified from this link.
coverageFiles <- list.files(pattern = "*bedgraph") #Create a file list for all 10 files to import
make.names(gsub("s1_R1_val_1_bismark_bt2_pe.deduplicated.bismark.cov_", "", coverageFiles))), read.table),
envir = .GlobalEnv) #Import files with list2env. Use lapply to setNames of the files by taking all the common parts of their names out. Files will be named zr2096_#_5x.bedgraph
I used the plotrix package to add an axis break to a grouped bar plot.
Artificially grouping bars to create a grouped bar plot with an axis break: https://stackoverflow.com/questions/24202245/grouped-barplot-with-cut-y-axis
Google lead me to a solution from Katie Lotterhos! I found it extremely useful.