In atusy/qntmap: Enhance quantitative analysis of EPMA map

wd <- tempdir()
knitr::opts_chunk$set(
  root.dir = wd,
  fig.width = 7,
  fig.height = 7,
  collapse = TRUE,
  comment = "#>"
)
library(knitr)
library(data.table)
library(captioner)
tbl_n <- captioner(prefix = "Tab.")
extdata <- system.file(package = "qntmap", "extdata")

Intro

This article introduces workarounds for errors from read_qnt() and read_xmap() when files recording analytical conditions are missing or written in incompatible formats depending on instruments (i.e., versions of EPMA hardware and software).

Spot analysis data

Among the required files to read spot analysis data (r tbl_n("qnt-files", display = "cite")), .cnd/elemw.cnd and Pos_001/data001.qnt can be missing or be written in unexpected format. In such case, prepare a csv file describing element names, dwell time for peak and background, and relative positions of backgrounds in a given format (r tbl_n("qnt-meta", display = "cite")). Then, following code will read spot analysis data.

qnt <- read_qnt(".qnt", conditions = "conditions_qnt.csv")
# First argument is path to the directory containing required files.
# "conditions" argument is a path to a user-prepared csv file.

.cap = tbl_n(
    name = "qnt-files", 
    caption = paste0(
      "[]{#tbl-qnt-files}",
      "Required files to retrieve spot analysis data"
    )
  )
kable(fread(file.path(extdata, "files-qnt.csv")), caption = .cap)

.cap = tbl_n(
    name = "qnt-meta", 
    caption = paste0(
      "[]{#qnt-meta}",
      "An example csv file which records element names, ",
      "dwell time for peak and background, and relative positions of backgrounds. ",
      "[Download csv file from here.](https://raw.githubusercontent.com/atusy/qntmap/master/inst/extdata/minimal/conditions_qnt.csv)"
    )
  )
kable(fread(file.path(extdata, "minimal", "conditions_qnt.csv")), caption = .cap)

Mapping data

Mapping data are expected to be saved as ASCII converted files (*.txt or *.csv) and as condition files (*.cnd) (r tbl_n("map-files", display = "cite")). Asterisks are expected to be filled by the format of #_map or by data# where sharps are integers. File names of ASCII converted files and condition files must be paired (e.g, 1_map.txt and 1_map.cnd). In case of irregular file names or missing condition files, prepare a csv file describing element name, file path, instrument, dwell time, probe current, X-Y coordinates of a starting pixel, step size, map size, and dead time (r tbl_n("map-meta", display = "cite")). Then, following code will read spot analysis data.

xmap <- read_qnt(conditions = "conditions_xmap.csv")
# "conditions" argument is a path to a user-prepared csv file.

.cap = tbl_n(
    name = "map-files", 
    caption = paste0(
      "[]{#tbl-map-files}",
      "Required files to retrieve mapping data"
    )
  )
kable(fread(file.path(extdata, "files-map.csv")), caption = .cap)

.cap = tbl_n(
    name = "map-meta", 
    caption = paste0(
      "[]{#map-meta}",
      "An example csv file which records element names, ",
      "dwell time for peak and background, and relative positions of backgrounds. ",
      "Except for 'Element' and 'File path', only values in a first row is used. ",
      "The other cells are ignored regardless of their contents. ",
      "[Download csv file from here.](https://raw.githubusercontent.com/atusy/qntmap/master/inst/extdata/minimal/conditions_xmap.csv)"
    )
  )
kable(fread(file.path(extdata, "minimal", "conditions_xmap.csv")), caption = .cap)