accessor function

R/XcmsExperiment.R

@@ -1378,17 +1378,16 @@ setMethod(
 
         # Check if user as ran matching lama vs chrompeaks beforehand
         if(length(param@rtMap) == 0)
-            rtMap <- matchLamasChromPeaks(object, param)
-        else
-            rtMap <- param@rtMap
+            param <- matchLamasChromPeaks(object, param)
+        rtMap <- param@rtMap
         if(length(rtMap) != length(object))
-            stop("The mismatch betweent the number of files matched to lamas ",
-            "and files in the object.")
+            stop("Mismatch between the number of files matched to lamas: ",
+                 length(rtMap), "and files in the object: ", length(object))
 
         # Make model and adjust retention for each file
         rt_adj <- bpmapply(rtMap, rt_raw, idx, FUN = function(x, y, i, param) {
             if (nrow(x) >= 10) { # too strict ? Gam always throws error when less than that and loess does not work that well either.
-                .adjust_rt_model(y, method = param@method,
+                xcms:::.adjust_rt_model(y, method = param@method,
                                  rt_map = x, span = param@span,
                                  resid_ratio = param@outlierTolerance,
                                  zero_weight = param@zeroWeight,

R/do_adjustRtime-functions.R

@@ -867,6 +867,15 @@ summarizeLamaMatch <- function(param){
     x
 }
 
+#' Function to access rtMap from `LamaParama` object
+rtMap <- function(x){
+    if(!inherits(x, "LamaParama"))
+        stop("The inputs need to be of class LamaParama")
+    rtMap <- param@rtMap
+    rtMap
+}
+
+
 ## phili: need to move that to a better file because its a method
 #' @title Plot summary of information of matching lamas to chromPeaks
 #'
@@ -886,14 +895,13 @@ setMethod("plot", "LamaParama", function(x, index = 1L, colPoints = "#00000060",
                                          xlab = "Matched Chromatographic peaks",
                                          ylab = "Lamas",
                                          main = NULL,...){
-    model <- .rt_model(method = param@method,
+    model <- xcms:::.rt_model(method = param@method,
                        rt_map= x@rtMap[[index]], span = param@span,
                        resid_ratio = param@outlierTolerance,
                        zero_weight = param@zeroWeight,
                        bs = param@bs)
     x <- x@rtMap[[index]]
-    callNextMethod(x = x, col = colPoints, xlab = xlab,
-                   ylab = ylab, main = main, ...) #not working and not sure why
-    #plot(obs, ref, type = type, xlab = xlab, ylab = ylab, col = "blue", main = main)
+    plot(x, type = "p", xlab = xlab, ylab = ylab, col = "blue",
+         main = main)
     points(model, type = "l", col = "black")
 })

tests/testthat/test_do_adjustRtime-functions.R

@@ -391,3 +391,11 @@ test_that("summarizeLamaMatch works", {
     expect_equal(nrow(res), length(tst))
     expect_equal(ncol(res), 7)
 })
+
+test_that("Accessing rtMap from LamaParama object works", {
+    param <- LamaParama(lamas = ref_mz_rt, toleranceRt = 10)
+    param <- matchLamasChromPeaks(tst, param)
+    expect_error(rtMap(ObiwarpParam()), "class")
+    rtMap <- rtMap(param)
+    expect_equal(length(rtMap), length(param@rtMap))
+})

vignettes/xcms.Rmd

@@ -136,7 +136,6 @@ performance. See the package vignette from the `r Biocpkg("Spectra")` package or
 the [SpectraTutorials](https://jorainer.github.io/SpectraTutorials) tutorial for
 more details on `Spectra` backends and how to change between them.
 
-
 ## Initial data inspection
 
 The `MsExperiment` object is a simple and flexible container for MS
@@ -1384,20 +1383,23 @@ It can be run before adjusting as well.
 
 ```{r}
 param <- matchLamasChromPeaks(tst, param = param)
+rtMap <- rtMap(param)
 
-summary <- summaryLama(param)
-
-plot(param)
 #' BPC of the first sample with matches to lamas overlay
 par(mfrow = c(1, 1))
 plot(bpc[1, 1], col = "#00000080", main = "Distribution CP matched to Lamas")
 points(rtime(bpc_tst_adj[1, 1]), intensity(bpc_tst_adj[1, 1]), type = "l",
        col = "#0000ff80")
 grid()
 abline(v = rtMap[[1]]$obs)
-```
 
-### add diagnostic part: see that later
+#access summary of matches and model information
+summary <- summarizeLamaMatch(param)
+summary[1]
+
+# Plot obs vs. ref with fitting line 
+plot(param)
+```
 
 # Additional details and notes