write_xlsx: Writes xlsx table
In USEPA/LUMA: LCMS-Based Untargeted Metabolomics Assistant

Description Usage Arguments Value Examples

Write xlsx table output from plot_metgroup. Essentially a wrapper for openxlsx::saveWorkbook

1	write_xlsx(validate.sheets, file.base, myname, mysheets)

`validate.sheets`	list of sheets to write to xlsx file. Currently must be of length 2
`file.base`	character return from `gen_filebase`.
`myname`	character string to append to file.base to name xlsx file
`mysheets`	character vector to name sheets in xlsx file. Currently must be of length 2. Default is `c("clear","muddy")`

Workbook from the openxlsx package

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

  # is case sensitive on Linux
  file <- system.file("extdata","Sample_Class.txt", package = "lcmsfishdata")
  Sample.df <- read.table(file, header = TRUE, sep = "\t")
  file2 <- system.file("extdata","CAMERA_objects_Pos.Rdata", package =
  "lcmsfishdata") # is case sensitive on Linux
  load(file2, envir = environment())
  Peak.list <- lcmsfishdata::Peaklist_Pos[["input_parsed"]]
  # is case sensitive on Linux
  file3 <- system.file("extdata","Sample_Data.csv", package = "lcmsfishdata")
  sample_data <- read.table(file3, header = TRUE, sep = ",")
  mzdatafiles <- sample_data$CT.ID

  file.base <- gen_filebase(mzdatafiles = mzdatafiles, BLANK = FALSE, IonMode
  = "Positive", ion.id = c("Pos","Neg"))

  mylist <- plot_metgroup(CAMERA.obj = anposGa, Sample.df = Sample.df,
  Peak.list = Peak.list, center = 2, BLANK = FALSE, gen.plots = FALSE,
  IonMode = "Positive", file.base = file.base, QC.id = "Pooled_QC", maxlabel
  = 10)
  class(mylist) ##is list
  length(mylist) ## with 2 elements
  validate.sheets <- mylist[[2]]
  myname <- "Validate_Metabolite_Groups"
  test <- write_xlsx(validate.sheets = validate.sheets, file.base = file.base, myname = myname)
  class(test) #returns Workbook object from the openxlsx package
  file.remove(paste(file.base, paste(myname,".xlsx", sep = ""), sep = "_"))
  }