New visualizeQFeatures function

DESCRIPTION

@@ -6,11 +6,11 @@ Authors@R:
     person(given =  "Loïc", family = "Guille", email = "loic.guille@uclouvain.be", comment = c(ORCID = "0000-0002-8387-1092"), role = c("aut")),
     person(given =  "Laurent", family = "Gatto", email = "laurent.gatto@uclouvain.be", comment = c(ORCID = "0000-0002-1520-2268"), role = c("ctb")),
     person("e-OMIX", role = c("fnd")))
-Description: QFeaturesGUI is a suite of shiny apps that serve as graphical interfaces for the QFeatures package. The package currently has two apps, importQFeatures and processQFeatures.
+Description: QFeaturesGUI is a suite of shiny apps that serve as graphical interfaces for the QFeatures package. The package provides three apps: import, process, and visualise.
 biocViews: Software, ShinyApps, GUI, Proteomics, SingleCell, DataImport, Preprocessing
 URL: https://rformassspectrometry.github.io/QFeaturesGUI/, https://github.com/rformassspectrometry/QFeaturesGUI
 BugReports: https://github.com/rformassspectrometry/QFeaturesGUI/issues
-License: MIT + file LICENSE
+License: GPL (>= 3)
 Encoding: UTF-8
 LazyData: false
 Imports:

NAMESPACE

@@ -1,7 +1,11 @@
 # Generated by roxygen2: do not edit by hand
 
+export(import)
 export(importQFeatures)
+export(process)
 export(processQFeatures)
+export(visualise)
+export(visualizeQFeatures)
 importFrom(DT,
   dataTableOutput,
   datatable,
@@ -14,7 +18,8 @@ importFrom(MsCoreUtils,
 importFrom(MultiAssayExperiment,
   ExperimentList,
   MultiAssayExperiment,
-  getWithColData
+  getWithColData,
+  longForm
 )
 importFrom(QFeatures,
   QFeatures,
@@ -48,12 +53,19 @@ importFrom(dplyr,mutate)
 importFrom(ggplot2,
   aes,
   annotate,
+  element_text,
+  facet_grid,
   geom_boxplot,
   geom_histogram,
+  geom_line,
+  geom_point,
   geom_violin,
   geom_vline,
   ggplot,
-  scale_x_continuous
+  scale_x_continuous,
+  scale_x_discrete,
+  theme,
+  theme_minimal
 )
 importFrom(htmltools,
   HTML,
@@ -178,7 +190,8 @@ importFrom(shinyjs,
 )
 importFrom(stats,
   as.formula,
-  na.exclude
+  na.exclude,
+  setNames
 )
 importFrom(tibble,rownames_to_column)
 importFrom(tidyr,pivot_longer)

NEWS.md

@@ -2,6 +2,11 @@
 
 ## QFeaturesGUI 0.99.3
 
+- Rename the app launchers to `import()`, `process()`, and `visualise()`.
+  The old names `importQFeatures()`, `processQFeatures()`, and
+  `visualizeQFeatures()` remain available as deprecated wrappers and warn
+  with the replacement function name.
+
 - Use default for argument `row.names` when using `read.table`.
 
 ## QFeaturesGUI 0.99.2

R/build_import_server.R

@@ -5,7 +5,7 @@
 #' @param input_table a dataframe that contains
 #'  the input table given by the user
 #'
-#' @return return the server function for the importQFeatures app.
+#' @return return the server function for the import app.
 #' @rdname INTERNAL_build_import_server
 #' @keywords internal
 #'

R/build_import_ui.R

@@ -1,6 +1,6 @@
 #' UI builder for import app
 #'
-#' @return A shiny dashboard UI for importQFeatures app
+#' @return A shiny dashboard UI for import app
 #' @rdname INTERNAL_build_import_ui
 #' @keywords internal
 #'
@@ -14,7 +14,7 @@
 build_import_ui <- function() {
     ui <- dashboardPage(
         skin = "blue",
-        header = header("importQFeatures"),
+        header = header("import"),
         dashboardSidebar(disable = TRUE, minified = FALSE, width = 0),
         dashboardBody(
             useShinyjs(),