ask_save.plot_QC.SBA: plot for basic QC of SBA data
In Rundmus/BAf-R_package: Binder Array data hanlding package in facility

Description Usage Arguments Value Author(s)

Generate plots to check basic QC of SBA data. This invokes other plot_QC functions, such as plot_QC_sample_signal_boxplot, plot_QC_binder_signal_boxplot, plot_QC_repl_var, and plot_QC_bead_count_boxplot

ask_save.plot_QC.SBA(
  baf,
  prefix = deparse(substitute(baf)),
  path = "../output/QC",
  bead_count = NULL,
  sample_order = order(batch(baf, "sample")),
  color_tbl_b = default_color_SBA_bead(T),
  color_tbl_s = default_color_SBA_ctrl_samples(sid(baf)),
  main = paste(unique(batch(baf, "binder")), collapse = ", "),
  ylab_signal = "Raw MFI",
  guide_line = TRUE
)

`baf`	an object of the `BAf-class` that contains SBA data
`prefix`	a prefix of generating files of basic QC plots. Often, it is sample layout ID.
`path`	path where the plots will be saved
`bead_count`	1) a `data.frame`, 2) a file name or 3) a `matrix`. check `plot_QC_bead_count_boxplot`
`sample_order`	the order of sample in plots. The default is the order by sample batch in order to easily check batch differences.
`color_tbl_b`	the colors of the binders employed for positive or negative control on plot. The information should be provided as a `data.frame`, in which columns are `name`, `reg` (regular expression to find the binder), `col` (color), and `type` (`positive` , `negative`, or `measure`). If this is given as NULL, it results in no coloring.
`color_tbl_s`	colors of samples on the plot. The information should be provided as a `data.frame` that has `name`, `reg` (regular expression to find the sample), `col` (color), `type` (`negative` or `replicated`). If this is NULL, then no coloring is applied.
`main`	same as `boxplot`
`ylab_signal`	the label of y-axis of the plots that show signal distribution in boxplots.
`guide_line`	if some guide lines of controls are displayed.