XICMasterPlotFcn_: Master Plotting function for plotting XIC's
In singjc/mstools: OpenSWATH Mass Spectrometry Data Exploration

Description Usage Arguments Value Author(s)

This function can be used to draw XIC's by calling getXIC

XICMasterPlotFcn_(
  dup_peps,
  uni_mod = NULL,
  sqMass_files,
  in_lib,
  in_osw,
  .osw_df = NULL,
  .lib_df = NULL,
  SCORE_IPF = FALSE,
  plotPrecursor = T,
  plotIntersectingDetecting = T,
  plotUniqueDetecting = F,
  plotIdentifying = F,
  plotIdentifying.Unique = F,
  plotIdentifying.Shared = F,
  plotIdentifying.Against = F,
  smooth_chromatogram = list(p = 4, n = 9),
  retention_time_limits = list(minRT = -Inf, maxRT = Inf),
  doFacetZoom = F,
  FacetFcnCall = NULL,
  doPlot = T,
  Charge_State = NULL,
  N_sample = 1,
  idx_draw_these = NULL,
  store_plots_subdir = "/Results/",
  printPlot = F,
  use_top_trans_pep = F,
  transition_selection_list = NULL,
  show_n_transitions = NULL,
  show_transition_scores = FALSE,
  annotate_best_pkgrp = TRUE,
  show_all_pkgrprnk = T,
  show_peak_info_tbl = F,
  show_manual_annotation = NULL,
  show_legend = T,
  mzPntrs = NULL
)

`dup_peps`	A character vector of a peptide sequence(s).
`uni_mod`	A character vector of a modified peptide sequence. (Default: NULL) If using this argument, dup_peps must be a single peptide
`sqMass_files`	A list of character vectors. Full paths to chromatogram file(s).
`in_lib`	A character vector. Full path to a pqp assay library.
`in_osw`	A character vector. Full path to an osw results file.
`.osw_df`	(data.table) A data.table object that contains the osw results peak group scores data
`.lib_df`	(data.table) A data.table object that contains lib information
`SCORE_IPF`	Do you want to extract IPF Score if present? (Default: FALSE. will use MS2 m-scores)
`plotPrecursor`	A logical value. True will plot precursor chromatogram
`plotIntersectingDetecting`	A logcail value. True will plot intersecting detecting transitions if comparing two peptidoforms.
`plotUniqueDetecting`	A logical value. True will plot unique detecting transitions if comparing two peptidoforms.
`plotIdentifying`	A logical value. True will plot identifying transitions.
`plotIdentifying.Unique`	A logical value. True will plot unique identifying transitions.
`plotIdentifying.Shared`	A logical value. True will plot shared identifying transitions. (Decaprecated)
`plotIdentifying.Against`	A logical value. True will plot against identifying transitions. (Decaprecated)
`smooth_chromatogram`	A list containing p (numeric) for the polynomial order for sgolay, and n (numeric) the bandwidth for sgolay. (Defualt: list(p=4, n=9)
`doFacetZoom`	A logical valie. Should the plot be zoomed in. The default zooming operation is based on the max int divided by 4. (Default: FALSE)
`FacetFcnCall`	A facet_zoom function with user defined parameters. i.e. FacetFcnCall = facet_zoom(xlim = c(7475, 7620), ylim = c(0, 4000) ). (Default: NULL)
`doPlot`	A logical value. TRUE will perform steps to save the plot as a pdf.
`Charge_State`	A numeric value. The target charge state. (Default: NULL)
`N_sample`	A numeric value. The number of peptidoforms to sample, if more than one. (Default: 1)
`idx_draw_these`	A vector of numeric values. The indices for the peptidoforms you wish to exaine.
`store_plots_subdir`	A character vector. The location to store plots.
`printPlot`	A logical value. TRUE will print plot in RStudio display.
`use_top_trans_pep`	A logical value. TRUE will rank the transitions based on the posterior error probabilities.
`transition_selection_list`	A list containing transitions to display for unique identifying. i.e. transition_selection_list <- list( y = c(3), b = c(8:10) )
`show_n_transitions`	A numeric value. Show n number of transitions
`show_transition_scores`	A logical value. If set to TRUE, will include TRANSITION PEPs as text tag when using interactive plotly.
`annotate_best_pkgrp`	A logical value. Annotate Top Peak Group
`show_all_pkgrprnk`	A logical value. Show all feature peak-group ranks. Usually 5. (Default: 5)
`show_manual_annotation`	A dataframe with leftWidth and rightWidth retention time boundary values of a manually annotated peak. Will draw a transparent blue shaded rectangle indicating manual annotation. I.e data.frame(leftWidth=300, rightWidth=330)
`show_legend`	A logical value. Display legend information for transition id, m/z and charge. (Default: TRUE)
`mzPntrs`	A list object containing cached mzR objects.