getXIC: Plot and Extracted Ion Chromatogram This function can be used...

In ArshiaMahmoodi/DrawAlignR: Visualizes Aligned Ms2 Chromatograms

Description

Plot and Extracted Ion Chromatogram This function can be used to plot an Extracted Ion Chromatogram

Usage

getXIC(
  graphic_obj,
  mod,
  df_lib,
  chromatogram_file,
  in_osw = NULL,
  transition_type = "detecting",
  intersecting_mz = NULL,
  uni_mod_list = NULL,
  max_Int = NULL,
  smooth_chromatogram = TRUE,
  doFacetZoom = FALSE,
  FacetFcnCall = NULL,
  top_trans_mod_list = NULL,
  Isoform_Target_Charge = NULL,
  RT_pkgrps = NULL,
  plotIdentifying.Unique = NULL,
  plotIdentifying.Shared = NULL,
  plotIdentifying.Against = NULL,
  show_n_transitions = NULL,
  show_legend = T,
  verbosity = 0
)

Arguments

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)
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?
@TODO	will add more decriptions for other params soon
df	A data.frame/data.table/matrix object to check for number of rows
msg	error message to return
numeric_obj	Check if an numeric object is not NULL a

Value

A list containing graphic_obj = the graphic handle for the ggplot filled with data and max_Int = the maximun intensity

if data.frame has 0 rows, return true, otherwise return false

If numeric object is not null, round numeric object to 4 digits

Author(s)

Justin Sing https://github.com/singjc

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

ArshiaMahmoodi/DrawAlignR documentation built on Jan. 6, 2022, 8:51 a.m.