lightweight exmaples for plot_mol_boxplot & loadings plot

ahmohamed · Apr 1, 2019 · 36c9eef · 36c9eef
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commit 36c9eef
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Showing 5 changed files with 17 additions and 7 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: lipidr
 Title: Lipidomics Analysis Workflow in R
-Version: 0.99.1
+Version: 0.99.2
 Authors@R: c(
     person(
         "Ahmed", "Mohamed", 

diff --git a/R/opls.R b/R/opls.R
@@ -307,7 +307,7 @@ plot_mva <- function(mvaresults, components = c(1, 2), color_by = NULL) {
 #'   data_normalized,
 #'   method = "OPLS-DA", group_col = "BileAcid", groups = c("water", "DCA")
 #' )
-#' plot_mva_loadings(mvaresults, color_by = "Class", top.n = 30)
+#' plot_mva_loadings(mvaresults, color_by = "Class", top.n = 10)
 plot_mva_loadings <- function(mvaresults, components = c(1, 2),
                               color_by = NULL,
                               top.n = nrow(mvaresults$loadings)) {

diff --git a/R/plot.R b/R/plot.R
@@ -336,8 +336,13 @@ plot_molecule_cv <- function(data, measure = "Area", log = TRUE) {
 #' @examples
 #' data(data_normalized)
 #' 
-#' plot_molecule_boxplot(data_normalized)
-#' plot_molecule_boxplot(data_normalized, "Retention.Time", log = FALSE)
+#' # plot the variation in intensity of ITSD (internal standards) in QC samples
+#' d_itsd_qc <- data_normalized[
+#'   rowData(data_normalized)$itsd,
+#'   data_normalized$group == "QC"
+#' ]
+#' plot_molecule_boxplot(d_itsd_qc)
+#' plot_molecule_boxplot(d_itsd_qc, "Retention.Time", log = FALSE)
 plot_molecule_boxplot <- function(data, measure = "Area", log = TRUE) {
   stopifnot(inherits(data, "SkylineExperiment"))
   dlong <- to_long_format(data, measure)

diff --git a/man/plot_molecule_boxplot.Rd b/man/plot_molecule_boxplot.Rd
diff --git a/man/plot_mva_loadings.Rd b/man/plot_mva_loadings.Rd