getXIC: Plot and Extracted Ion Chromatogram
In singjc/mstools: OpenSWATH Mass Spectrometry Data Exploration

Description Usage Arguments Value Author(s)

This function can be used to plot an Extracted Ion Chromatogram

Check Dataframe, if empty return an object and stop function call

Check numeric values if not NULL

getXIC(
  graphic_obj = ggplot2::ggplot(),
  mod,
  df_lib,
  chromatogram_file,
  chromatogram_data_points_list = NULL,
  Isoform_Target_Charge,
  in_osw = NULL,
  df_osw = NULL,
  SCORE_IPF = FALSE,
  annotate_best_pkgrp = TRUE,
  transition_type = c("detecting"),
  uni_mod_list = NULL,
  max_Int = NULL,
  retention_time_limits = list(minRT = -Inf, maxRT = Inf),
  smooth_chromatogram = list(p = 4, n = 9),
  doFacetZoom = FALSE,
  FacetFcnCall = NULL,
  top_trans_mod_list = NULL,
  transition_selection_list = NULL,
  RT_pkgrps = NULL,
  show_manual_annotation = NULL,
  show_peak_info_tbl = F,
  plotIdentifying.Unique = NULL,
  plotIdentifying.Shared = NULL,
  plotIdentifying.Against = NULL,
  show_n_transitions = NULL,
  transition_dt = NULL,
  show_legend = T,
  mzPntrs = NULL
)

`graphic_obj`	A ggplot() graphics handle. Initialize with g <- ggplot() to create an empty ggplot handle
`mod`	A character vector for specific peptide/modified peptide to extract I.e. 'ANSSPTTNIDHLK'/'ANS(UniMod:21)SPTTNIDHLK(UniMod:259)'. The MODIFIED_SEQUENCE column is used
`df_lib`	A data.table containing spectral library information
`chromatogram_file`	A character vector of the absolute path and filename of the chromatogram file. (Must be .mzML or sqMass format)
`chromatogram_data_points_list`	(Optional) Pass a list containing chromatogram data.
`in_osw`	A character vector of the absolute path and filename of the OpenSwath Output file. (Must be .osw) @TODO maybe make this more robust for tsv files as well?
`df_osw`	An optional dataframe containing OpenSwath Results information. (Use this if you have a dataframe cached in memory)
`SCORE_IPF`	Do you want to extract IPF Score if present? (Default: FALSE. will use MS2 m-scores)
`annotate_best_pkgrp`	Annotate the ebst peak group
`transition_type`	A vector containing possible choices for dispalying one of the following transition group types. getXIC needs to be called for each option (Options: c('precursor', 'detecting', 'identifying') )
`max_Int`	A numeric value indicating the maximum intensity. This is used for FacetZooming the y-axis. (Default: NULL)
`smooth_chromatogram`	A list object containing the polynomial filter order (p), and the bandwidth (number of data-points to smooth over, n). (Default: list(p=4, n=9))
`doFacetZoom`	A logical value for calling Facet_Zoom function to zoom in the y axis based on the max_Int/4. (Default: FALSE)
`FacetFcnCall`	A personalized function call to Facet_Zoom. I.e. FacetFcnCall = facet_zoom(xlim = c(3950, 4050), ylim = c(0, 10000)). (Default: NULL)
`top_trans_mod_list`	A list containing a data.table/data.frame of the current peptide(mod peptide) with information for transition ids and top 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) )
`RT_pkgrps`	A numeric vector of the alternative peak group ranks to display. I.e. c(2, 4) (Default: NULL)
`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_peak_info_tbl`	A logical value. Show peak information table containing RT, rank, ms2-mscore, ipf_pep, ipf-mscore. (Default: FALSE)
`plotIdentifying.Unique`	A logical value. TRUE will plot unique identifying transitions. (Default: NULL)
`plotIdentifying.Shared`	A logical value. TRUE will plot shared identifying transitions. (Default: NULL)
`plotIdentifying.Against`	A logical value. TRUE will plot against identifying transitions. (Default: NULL)
`show_n_transitions`	A numeric value indicating the number of transitions to draw. (Default: NULL, default is 6 transitions)
`transition_dt`	A data.table containing TRANSITION_SCORE Information obtained from the OSW file using getTransitionScores_. (Default: NULL)
`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.
`unit_mod_list`	A list of potential modifiable forms. (Default: NULL)
`df`	A data.frame/data.table/matrix object to check for number of rows
`return_item`
`msg`	error message to return
`numeric_obj`	Check if an numeric object is not NULL
`signif.not`	Return significant notation