write_xlsx: Writes xlsx table

In jmosl01/LUMA: LCMS-Based Untargeted Metabolomics Assistant

Description

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

Usage

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

Arguments

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")

Value

Workbook from the openxlsx package

Examples

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 = "_"))
  }

jmosl01/LUMA documentation built on Sept. 2, 2020, 6:20 a.m.