fix: check_data_format

Author: ethanbass

R/call_aston.R

@@ -86,7 +86,7 @@ uv_converter <- function(path, format_out = c("matrix","data.frame","data.table"
   if (data_format == "long"){
     x <- reshape_chrom(x, data_format = "long")
   }
-  x <- convert_chrom_format(x, format_out = format_out)
+  x <- convert_chrom_format(x, format_out = format_out, data_format)
   if (correction){
     # multiply by empirical correction value
     correction_value <- 0.9536743164062551070259132757200859487056732177734375
@@ -127,7 +127,7 @@ trace_converter <- function(path, format_out = c("matrix", "data.frame"),
   if (data_format == "long"){
     x <- reshape_chrom(x, data_format = "long")
   }
-  x <- convert_chrom_format(x, format_out = format_out)
+  x <- convert_chrom_format(x, format_out = format_out, data_format)
   x
 }
 

R/call_entab.R

@@ -51,7 +51,7 @@ call_entab <- function(path, data_format = c("wide", "long"),
     colnames(x)[c(1, 3)] <- c("rt", "intensity")
     data_format <- "long"
   }
-  x <- convert_chrom_format(x, format_out = format_out)
+  x <- convert_chrom_format(x, format_out = format_out, data_format)
   if (read_metadata){
     meta <- r$metadata()
     meta$run_date <- as.POSIXct(eval(meta$run_date))

R/read_chemstation_csv.R

@@ -27,7 +27,7 @@ read_chemstation_csv <- function(path, format_out = c("matrix", "data.frame",
                                  data_format = c("wide", "long"),
                                  read_metadata = TRUE){
   format_out <- check_format_out(format_out)
-  data_format <- match.arg(data_format, c("wide", "long"))
+  data_format <- check_data_format(data_format, format_out = format_out)
   data <- read.csv(path, row.names = 1, header = TRUE,
                 fileEncoding = "utf-16LE", check.names = FALSE)
 

R/read_shimadzu_ascii.R

@@ -62,7 +62,7 @@ read_shimadzu <- function(path, what = "chroms",
   include <- match.arg(include, c("fid", "lc", "dad", "uv", "tic", "status"),
                        several.ok = TRUE)
   format_out <- check_format_out(format_out)
-  data_format <- match.arg(data_format, c("wide", "long"))
+  data_format <- check_data_format(data_format, format_out)
   peaktable_format <- match.arg(peaktable_format, c("chromatographr", "original"))
   metadata_format <- match.arg(metadata_format, c("chromconverter", "raw"))
   ms_format <- match.arg(ms_format, c("data.frame", "list"))

R/utils.R

@@ -7,6 +7,19 @@ check_format_out <- function(format_out){
   match.arg(format_out, c("matrix", "data.frame", "data.table"))
 }
 
+#' Check Data Format Argument
+#'
+#' Make sure that \code{data_format} argument is "long" when \code{format_out} is
+#' \code{"data.table"}.
+#' @noRd
+
+check_data_format <- function(data_format, format_out){
+  if (format_out == "data.table"){
+    data_format <- "long"
+  }
+  match.arg(data_format, c("wide", "long"))
+}
+
 #' Convert chromatogram format
 #' @author Ethan Bass
 #' @noRd

tests/testthat/test-read_chroms.R

@@ -17,7 +17,7 @@ test_that("chromConverter can read `Agilent Chemstation` .csv file", {
   x1 <- read_chroms(path_csv, format_in = "chemstation_csv",
                     format_out = "data.table", progress_bar = FALSE)[[1]]
   expect_s3_class(x1, "data.table")
-  expect_equal(colnames(x1), c("rt", "220.00000"))
+  expect_equal(colnames(x1), c("rt", "intensity"))
   expect_equal(attr(x1, "data_format"), "long")
   expect_equal(attr(x1, "format_out"), "data.table")
 
@@ -156,18 +156,16 @@ test_that("`Shimadzu` ASCII parser works", {
   expect_s3_class(x1, "data.table")
   expect_equal(attr(x1, "format_out"), "data.table")
   expect_equal(attr(x1, "data_format"), "long")
-  expect_equal(dim(x1),c(66255,2))
+  expect_equal(dim(x1),c(66255,3))
 
   x2 <- read_chroms(path, format_in = "shimadzu_fid", find_files = FALSE,
-                    progress_bar = FALSE, format_out="data.frame")[[1]]
+                    progress_bar = FALSE, format_out="data.frame",
+                    data_format = "long")[[1]]
   expect_s3_class(x2, "data.frame")
   expect_equal(attr(x2, "format_out"), "data.frame")
-  expect_equal(attr(x2, "data_format"), "wide")
-  expect_equal(dim(x2),c(66255,1))
-  expect_equal(x1,x2)
-
-  # long format doesn't work
-  # maybe because there's nothing to add?
+  expect_equal(attr(x2, "data_format"), "long")
+  expect_equal(dim(x2),c(66255,3))
+  expect_equal(x1, x2, ignore_attr=TRUE)
 })
 
 test_that("read_mzml works", {