plot_ionduplicate: Loop-based EIC Plotter for Ion Mode Duplicates
In USEPA/LUMA: LCMS-Based Untargeted Metabolomics Assistant

Description Usage Arguments Value Examples

Plots EICs from ion mode duplicates using plotEICs-methods from CAMERA.

plot_ionduplicate(
  anposGa,
  xpos,
  annegGa,
  xneg,
  rt.method,
  Peak.list,
  gen.plots,
  file.base,
  QC.id,
  mytable,
  maxEIC,
  maxQC,
  ...
)

`anposGa`	`xsannotate` object in parent environment with isotopes, ion adducts and fragments for positive mode.
`xpos`	`xcmsSet` object shoud have grouping, retention time correction and fillPeaks applied. Default is to look for this in `anposGa`.
`annegGa`	`xsannotate` object in parent environment with isotopes, ion adducts and fragments for negative mode.
`xneg`	`xcmsSet` object shoud have grouping, retention time correction and fillPeaks applied. Default is to look for this in `annegGa`.
`rt.method`	Which method to use for EIC. Can be one of `c("corrected","raw")`.
`Peak.list`	data.frame containing combined ion mode peaklist with column `"Duplicate_ID"`. Alternatively can be retrieved from databases. Default is `NULL`.
`gen.plots`	logical indicating whether to create plots for ion mode duplicates. Default is `FALSE`.
`file.base`	character string used to name graphical output. Default is `"EIC_plots"`.
`QC.id`	character identifier for pooled QC samples. Default is `"Pooled_QC"`.
`mytable`	character name of table in database to return
`maxEIC`	numeric Max number of features for which to `plotEICs` for each metabolite.
`maxQC`	numeric Max number of QCs used to `plotEICs`.
`...`	parameters to be passed to database functions

list of length 2 EIC indices for the ion duplicate plots

library(LUMA)
if(require(lcmsfishdata, quietly = TRUE)) {

file <- system.file("extdata","CAMERA_objects_Pos.Rdata", package =
"lcmsfishdata") # is case sensitive on Linux
load(file, envir = environment())
file2 <- system.file("extdata","CAMERA_objects_Neg.Rdata", package =
"lcmsfishdata") # is case sensitive on Linux
load(file2, envir = environment())

Peak.list <- lcmsfishdata::Peaklist_db[["Peaklist_Combined_with_Duplicate_IDs"]]

test <- plot_ionduplicate(anposGa = anposGa, annegGa = annegGa, Peak.list =
Peak.list, gen.plots = FALSE)
class(test) ##is list
length(test) ## with 2 elements

  ## Not run: 
  #Runs with pdf plotting. This requires access to raw datafiles and won't
  #work with lcmsfishdata. Better to use your own data here.
  test <- plot_ionduplicate(anposGa = anposGa, annegGa = annegGa, Peak.list =
  Peak.list, gen.plots = TRUE)

  
## End(Not run)
}