CI: add tests for Shimadzu tables

Author: ethanbass

R/read_peaklist.R

@@ -106,10 +106,10 @@ read_peaklist <- function(paths, find_files,
     data <- lapply(seq_along(data), function(i){
       if (inherits(data[[i]], "list")){
         lapply(data[[i]], function(xx){
-          cbind(Sample = file_names[i], xx)
+          cbind(sample = file_names[i], xx)
         })
       } else {
-        cbind(Sample = file_names[i], data[[i]])
+        cbind(sample = file_names[i], data[[i]])
       }
     })
     class(data) <- "peak_list"

tests/testthat/test-extra.R

@@ -592,6 +592,38 @@ test_that("read_chroms can read 'Shimadzu' PDA files (ASCII and LCD)", {
                round(attr(x2, "time_range"), 3))
 })
 
+test_that("Shimadzu Anthocyanin peak tables match", {
+  skip_on_cran()
+  skip_if_not_installed("chromConverterExtraTests")
+
+  path_ascii <- system.file("shimadzuDAD_Anthocyanin.txt",
+                            package = "chromConverterExtraTests")
+  skip_if_not(file.exists(path_ascii))
+
+  path_lcd <- system.file("Anthocyanin.lcd",
+                          package = "chromConverterExtraTests")
+  skip_if_not(file.exists(path_lcd))
+
+  x <- read_peaklist(path_ascii, format_in = "shimadzu_dad",
+                     data_format = "original",
+                   progress_bar = FALSE)[[1]]
+
+  x1 <- read_shimadzu_lcd(path_lcd, what="peak_table")
+  x1 <- read_peaklist(path_lcd, format_in = "shimadzu_lcd", progress_bar=FALSE)[[1]]
+
+  expect_equal(x[[1]][,c(3,6:7,4:5,8:9,11,13:18,21:22)],x1[[1]][,-1], tolerance=.001,
+            ignore_attr=TRUE)
+  expect_equal(x[[2]][,c(3,6:7,4:5,8:9,11,13:18,21:22)],x1[[3]][,-1], tolerance=.001,
+               ignore_attr=TRUE)
+  expect_equal(x[[3]][,c(3,6:7,4:5,8:9,11,13:18,21:22)],x1[[4]][,-1], tolerance=.001,
+               ignore_attr=TRUE)
+  expect_equal(x[[4]][,c(3,6:7,4:5,8:9,11,13:18,21:22)],x1[[5]][,-1], tolerance=.001,
+               ignore_attr=TRUE)
+  expect_equal(x[[5]][,c(3,6:7,4:5,8:9,11,13:18,21:22)],x1[[6]][,-1], tolerance=.001,
+               ignore_attr=TRUE)
+})
+
+
 test_that("read_chroms can read 2D chromatograms from 'Shimadzu' LCD files", {
   skip_on_cran()
   skip_if_not_installed("chromConverterExtraTests")
@@ -729,6 +761,36 @@ test_that("read_chroms can read multi-channel chromatograms from 'Shimadzu' LCD
   expect_equal(x2[x2$lambda == "", "intensity"], x[["B"]], ignore_attr = TRUE)
 })
 
+test_that("Shimadzu multichannel peak tables match", {
+  skip_on_cran()
+  skip_if_not_installed("chromConverterExtraTests")
+
+  path_asc <- system.file("multichannel_chrom.txt",
+                          package = "chromConverterExtraTests")
+
+  skip_if_not(file.exists(path_asc))
+
+  path_lcd <- system.file("multichannel_chrom.lcd",
+                          package = "chromConverterExtraTests")
+  skip_if_not(file.exists(path_lcd))
+
+  x <- read_peaklist(path_asc, format_in = "shimadzu_dad",
+                     data_format = "original",
+                     progress_bar = FALSE)[[1]]
+
+  x1 <- read_peaklist(path_lcd, format_in = "shimadzu_lcd",
+                      progress_bar=FALSE)[[1]]
+
+
+  expect_equal(x[[1]][,c(3,6:7,4:5,8:9,11,13:18,21:22)],x1[[1]][,-1], tolerance=.01,
+               ignore_attr=TRUE)
+  expect_equal(x[[2]][,c(3,6:7,4:5,8:9,11,13:18,21:22)],x1[[2]][,-1], tolerance=.001,
+               ignore_attr=TRUE)
+  expect_equal(x[[3]][,c(3,6:7,4:5,8:9,11,13:18,21:22)],x1[[3]][,-1], tolerance=.001,
+               ignore_attr=TRUE)
+})
+
+
 test_that("read_chroms can read 'Agilent' .dx files", {
   skip_on_cran()
   skip_if_not_installed("chromConverterExtraTests")
@@ -874,6 +936,26 @@ test_that("Shimadzu GCD parser works", {
   expect_equal(as.numeric(attr(txt, "time_range")), round(attr(x, "time_range"), 3))
 })
 
+test_that("Shimadzu FID peak tables match", {
+  skip_on_cran()
+  skip_if_not_installed("chromConverterExtraTests")
+
+  path_asc <- test_path("testdata/ladder.txt")
+
+  path_gcd <- system.file("FS19_214.gcd", package = "chromConverterExtraTests")
+  skip_if_not(file.exists(path_gcd))
+
+  x <- read_peaklist(path_asc, format_in = "shimadzu_dad",
+                     data_format = "original",
+                     progress_bar = FALSE)[[1]]
+
+  x1 <- read_peaklist(path_gcd, format_in = "shimadzu_gcd", progress_bar=FALSE)
+
+  expect_equal(x[,c(3,6:7,4:5,8:9,11,13:18,21:22)], x1[[1]][,-1], tolerance=.001,
+               ignore_attr=TRUE)
+})
+
+
 test_that("Shimadzu QGD parser works", {
   skip_on_cran()
   skip_if_missing_dependencies()

tests/testthat/test-read_chroms.R

@@ -298,10 +298,10 @@ test_that("read_peaklist can read `Shimadzu` fid files", {
   expect_equal(x[[1]][[1,"sample"]], "ladder")
   expect_equal(x[[1]][[1,"sample"]], "ladder")
   expect_equal(colnames(x[[1]]),
-               c("sample","Peak.","R.Time","I.Time","F.Time","Area","Height",
-                 "A.H","Conc.","Mark","ID.","Name", "k.", "Plate..", "Plate.Ht.",
-                 "Tailing", "Resolution", "Sep.Factor", "Area.Ratio", "Height.Ratio",
-                 "Conc...", "Norm.Conc."))
+               c("sample","Peak#","R.Time","I.Time","F.Time","Area","Height",
+                 "A/H","Conc.","Mark","ID#","Name", "k'", "Plate #", "Plate Ht.",
+                 "Tailing", "Resolution", "Sep.Factor", "Area Ratio", "Height Ratio",
+                 "Conc. %", "Norm Conc."))
   expect_equal(attr(x, "class"), "peak_list")
 })