fix: bug in mirror plot for 2D data

also added warning when automatically selecting factor levels

NEWS.md

@@ -1,7 +1,9 @@
 # chromatographR 0.7.1
 
 * Fixed bug in `get_peaks` causing peaks to erroneously filtered out in some cases.
-* Small updates to documentation (in `preprocess` and `fit_peaks` functions) to better describe arguments.
+* Made small updates to documentation (in `preprocess` and `fit_peaks` functions) to better describe arguments.
+* Added warning in `mirror_plot` when `var` contains more than two levels and levels aren't specified.
+* Fixed bug to allow `mirror_plot` to work properly with 2D data.
 
 # chromatographR 0.7.0
 

R/plot.peak_table.R

@@ -199,7 +199,7 @@ boxplot.peak_table <- function(x, formula, ...){
 #' @concept Visualization
 #' @export
 
-mirror_plot <- function(x, chrom_list, lambdas, var, subset = NULL,
+mirror_plot <- function(x, chrom_list, lambdas = NULL, var, subset = NULL,
                         print_legend = TRUE, legend_txt = NULL, legend_pos = "topright",
                         legend_size = 1, mirror = TRUE, xlim = NULL, ylim = NULL, ...){
   check_peaktable(x)
@@ -214,9 +214,11 @@ mirror_plot <- function(x, chrom_list, lambdas, var, subset = NULL,
   }
   if (missing(chrom_list)){
     chrom_list <- get_chrom_list(x)
-  } else get_chrom_list(x, chrom_list)
+  } else {
+    get_chrom_list(x, chrom_list)
+  }
   new.ts <- round(as.numeric(rownames(chrom_list[[1]])), 2)
-  if (ncol(x[[1]]) == 1){
+  if (ncol(chrom_list[[1]]) == 1){
     lambdas.idx <- 1
   } else {
     lambdas.idx <- sapply(lambdas, function(lambda){
@@ -234,6 +236,10 @@ mirror_plot <- function(x, chrom_list, lambdas, var, subset = NULL,
     }
   }
   if (is.null(subset)){
+    if (nlevels(fac)>2){
+      warning(paste0("Selecting first two levels of ", sQuote(var)), ". To choose different levels,
+              use the `subset` argument to specify the desired levels.")
+    }
     trt1 <- levels(fac)[1]
     trt2 <- levels(fac)[2]
   } else {
@@ -245,9 +251,9 @@ mirror_plot <- function(x, chrom_list, lambdas, var, subset = NULL,
   if (print_legend & is.null(legend_txt))
     legend_txt <- c(trt1,trt2)
   if (is.null(xlim))
-    xlim <- c(head(new.ts,1),tail(new.ts,1))
+    xlim <- c(head(new.ts, 1), tail(new.ts, 1))
   y_max <- max(sapply(chrom_list, function(xx){
-    max(xx[, as.character(min(as.numeric(lambdas)))], na.rm = TRUE)
+    max(xx[, lambdas.idx], na.rm = TRUE)
   }))
   if (mirror){
     if (is.null(ylim))

tests/testthat/test-pipeline.R

@@ -202,7 +202,9 @@ test_that("attach_metadata works", {
   expect_equal(colnames(pk_tab$sample_meta), colnames(meta))
 
   ### check errors & warnings ###
-  expect_error(attach_metadata(pk_tab))
+  expect_error(attach_metadata())
+  expect_error(attach_metadata(warp))
+  expect_error(attach_metadata(pk_tab, metadata = warp))
   expect_error(attach_metadata(pk_tab, metadata=meta, column ="x"))
   expect_error(attach_metadata(pk_tab$tab, metadata=meta, column ="vial"))
   expect_error(attach_metadata(pk_tab, metadata=rbind(meta,meta), column ="vial"))
@@ -217,6 +219,9 @@ test_that("attach_ref_spectra works", {
   pk_tab <- attach_ref_spectra(pk_tab, chrom_list = dat.pr, ref = "max.int")
   expect_equal(pk_tab$args[["reference_spectra"]], "max.int")
   expect_equal(colnames(pk_tab$tab), colnames(pk_tab$ref_spectra))
+
+  # test errors
+  expect_error(attach_ref_spectra(peak_table = warp))
   expect_error(attach_ref_spectra(pk_tab, chrom_list = dat.pr, ref = "x"))
 })