add LockMassCorrection plot method

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rawrr
 Type: Package
 Title: Direct Access to Orbitrap Data and Beyond
-Version: 1.11.5
+Version: 1.11.6
 Authors@R: c(person("Christian", "Panse",
         email = "[email protected]",
         role = c("aut", "cre"),
@@ -12,7 +12,7 @@ Authors@R: c(person("Christian", "Panse",
     comment = c(ORCID = "0000-0002-1847-885X")))
 Depends: R (>= 4.1)
 Imports:
-        grDevices, graphics, stats, utils
+        grDevices, graphics, stats, utils, ggplot2
 Suggests:
     BiocStyle (>= 2.5),
     ExperimentHub,

NAMESPACE

@@ -32,6 +32,14 @@ export(scanNumber)
 export(tic)
 export(validate_rawrrIndex)
 export(validate_rawrrSpectrum)
+importFrom(ggplot2,aes_string)
+importFrom(ggplot2,facet_wrap)
+importFrom(ggplot2,geom_hline)
+importFrom(ggplot2,geom_line)
+importFrom(ggplot2,ggplot)
+importFrom(ggplot2,labs)
+importFrom(ggplot2,scale_x_continuous)
+importFrom(ggplot2,theme_light)
 importFrom(grDevices,hcl.colors)
 importFrom(graphics,legend)
 importFrom(graphics,lines)

R/plot.R

@@ -0,0 +1,46 @@
+#R
+# contains selected rawDiag plot methods
+# 
+#' lock mass correction plot
+#' @inheritParams readFileHeader
+#' @return a ggplot object
+#' @author Christian Trachsel (2017), Christian Panse (2023)
+#' @references rawDiag \doi{10.1021/acs.jproteome.8b00173}
+#' @examples 
+#' rawrr::sampleFilePath() |> rawrr:::.plotLockMassCorrection()
+#' @importFrom ggplot2 ggplot aes_string geom_hline geom_line labs scale_x_continuous facet_wrap theme_light
+.plotLockMassCorrection <- function(rawfile){
+  stopifnot("LM m/z-Correction (ppm):" %in% rawrr::readTrailer(rawfile))
+
+  message("Plotting lock mass correction for ", basename(rawfile))
+  message("reading index for ", basename(rawfile), "...")
+
+  rawfile |> 
+    rawrr::readIndex() -> rawrrIndex
+
+  message("reading LM m/z-Correction (ppm) ...")
+  rawfile |> 
+    rawrr::readTrailer("LM m/z-Correction (ppm):") |> 
+    as.numeric() ->
+    LMCorrection
+
+  rawrrIndex$LMCorrection <- LMCorrection
+  rawrrIndex$rawfile <- basename(rawfile)
+
+  rawrrIndex |>
+    base::subset(rawrrIndex$MSOrder == "Ms") |>
+    ggplot2::ggplot(ggplot2::aes_string(x = "StartTime" , y = "LMCorrection")) +
+    ggplot2::geom_hline(yintercept = c(-5, 5), colour = "red3", linetype = "longdash") +
+    ggplot2::geom_line(size = 0.3) +
+    ggplot2::geom_line(stat = "smooth",
+                       method= "gam",
+                       formula = y ~ s(x, bs ="cs"),
+                       colour = "deepskyblue3", se = FALSE) +
+    ggplot2::labs(title = "Lock mass correction plot") +
+    ggplot2::labs(subtitle = "Plotting lock mass correction value versus retention time") +
+    ggplot2::labs(x = "Retention Time [min]", y = "Lock Mass Correction [ppm]") +
+    ggplot2::scale_x_continuous(breaks = base::pretty(8)) +
+    # scale_y_continuous(breaks = scales::pretty_breaks(8), limits = c(-10, 10)) +
+    ggplot2::facet_wrap(~ rawfile) +
+    ggplot2::theme_light()
+}