feat: include wavelength and retention time information in long tables

NEWS.md

@@ -1,3 +1,8 @@
+#chromatographR 0.7.3
+
+* Updated `reshape_peaktable` function to include wavelength and retention time data.
+* Updated `pk_tab` data file to latest peak table format.
+
 # chromatographR 0.7.2
 
 * Export `get_times` and `get_lambdas` functions.

R/reshape_chroms.R

@@ -99,7 +99,9 @@ reshape_peaktable <- function(x, peaks, metadata, fixed_levels = TRUE){
     times = colnames(df), timevar = "peak",
     idvar = "sample", ids = rownames(df))
   rownames(xx) <- NULL
-  xx <- xx[,c(3,1,2)]
+  xx <- merge(xx, data.frame(peak=colnames(x$pk_meta), t(x$pk_meta[c("lambda","rt"),])),
+        by="peak",all.x=TRUE)
+  xx <- xx[, c(1, 3, 4, 5, 2)]
   if (!is.null(dim(x$sample_meta))){
     xx <- merge(xx, data.frame(sample = row.names(df), x$sample_meta),
                 by = "sample", all.x = TRUE)

tests/testthat/test-utility-functions.R

@@ -118,11 +118,11 @@ test_that("reshape_peaktable works as expected",{
   pk_tab <- attach_metadata(pk_tab, metadata = meta, column = "vial")
 
   pktab_long <- reshape_peaktable(pk_tab)
-  expect_equal(ncol(pktab_long), 3 + ncol(pk_tab$sample_meta))
+  expect_equal(ncol(pktab_long), 5 + ncol(pk_tab$sample_meta))
   expect_equal(nrow(pktab_long), nrow(pk_tab)*ncol(pk_tab))
 
   pktab_long <- reshape_peaktable(pk_tab, peaks = c("V51","V60"), metadata = "trt")
-  expect_equal(ncol(pktab_long), 3 + 1)
+  expect_equal(ncol(pktab_long), 5 + 1)
   expect_equal(nrow(pktab_long), nrow(pk_tab)*2)
 })
 

vignettes/articles/fid_article.bib

@@ -119,7 +119,7 @@ @article{legan2021
 
 @article{legan2022,
   title = {Molecular and {{Chemical Basis}} of {{Social Olfaction}} in {{Polistes Paper Wasps}}},
-  author = {Legan, Andrew Wesley},
+  author = {Legan, Andrew W.},
   date = {2022},
   publisher = {Cornell University Library},
   doi = {10.7298/CZ0P-6J74}