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Feature:qplot.electrophoresis now offers the normalize = "window" option, which normalizes with only the data within the x-limits of the plot, as opposed to normalize = "total", which normalizes against the entire sample (between markers). See the updated vignette for example usage.
Feature:qplot.electrophoresis now offers the show.peaks = "markers" option, which fills in and color-codes the areas of only the marker peaks but not any other peaks. This can be useful if you include the markers in your plot (e.g. raw data electropherogram) and need to explain what they are but aren't otherwise interested in the reported peaks. See the updated vignette for example usage.
Important syntax change: In qplot.electrophoresis, normalize = TRUE is no longer accepted. That behavior, i.e. normalizing by the entire sample, now requires normalize = "total". Please update old scripts, or consider switching to the new normalize = "window" if that is more useful.
Important syntax change: In qplot.electrophoresis, show.peaks = FALSE is no longer accepted. That behavior, i.e. not filling in the area under any peaks, now requires show.peaks = "none". Please update old scripts, or consider switching to the new show.peaks = "markers" if that is more useful.
Syntax improvement:qplot.electrophoresis now uses match.arg for the normalize, geom, and show.peaks arguments so you can simplify them with unambiguous substrings (e.g. normalize = "w" instead of normalize = "window"). It does not use match.arg for the log argument because the options for that are not well suited (copied from ggplot2::qplot).