Dev (#3)

* clean up requirements
* sync package loading with req.txt file
* clean up redudant code to check and install packages
* set up tests for mzML and Bruker file loading
* set smoothHalfWindowSize to a more reasonable value
* remove devtools and use pak instead
* add more error handling for loading data
* add notifications to the app

.github/workflows/docker-publish.yml

@@ -44,13 +44,17 @@ jobs:
       # Install R package dependencies from req.txt
       - name: Install R packages from req.txt
         run: |
-          R -e "install.packages('devtools')"
-          R -e "devtools::install_github('CeMOS-Mannheim/MALDIcellassay')"
-          R -e "packages <- readLines('req.txt'); install.packages(packages)"
+          R -e "install.packages('pak')"
+          R -e "packages <- readLines('req.txt'); pak::pkg_install(packages)"
+
+       # Install R package dependencies from req.txt
+      - name: Install MALDIcellassay
+        run: |
+          R -e "pak::pkg_install('CeMOS-Mannheim/MALDIcellassay')"
 
       # Install testthat if it's not listed in req.txt
       - name: Install testthat
-        run: R -e "if (!require('testthat')) install.packages('testthat')"
+        run: R -e "if (!require('testthat')) pak::pkg_install('testthat')"
 
       # Run tests
       - name: Run tests

.gitignore

@@ -5,3 +5,4 @@
 defaults.conf
 settings.conf
 settings.csv
+checkUsedFunctions.R

Dockerfile

@@ -14,7 +14,8 @@ COPY req.txt /req.txt
 RUN R -e "packages <- readLines('/req.txt'); install.packages(packages)"
 
 # Install the MALDIcellassay from GitHub
-RUN R -e "devtools::install_github('CeMOS-Mannheim/MALDIcellassay')"
+RUN R -e "pak::pkg_install('CeMOS-Mannheim/MALDIcellassay')"
+
 
 ## copy app folder into container
 COPY ./ ./app

components/hcTab.R → components/clustTab.R

@@ -1,16 +1,16 @@
 clustTab <- function() {
-  #### HClust tab ####
+  #### clustering tab ####
   tabPanel("Cluster",
            h4("Curve clustering"),
            fluidRow(
              column(6,
-                    plotlyOutput("hclustPlot")),
+                    plotlyOutput("clustPlot")),
              column(6,
                     plotlyOutput("clustCurvesPlot"))
            ),
            fluidRow(
              column(2,
-                    createActionButton(inputId = "doHC",
+                    createActionButton(inputId = "doClust",
                                        label = "Perform clustering",
                                        icon = "circle-nodes")),
              column(2,
@@ -21,7 +21,7 @@ clustTab <- function() {
                                 value = defaults$num_cluster,
                                 step = 1)),
              column(2,
-                    createActionButton(inputId = "hc2peaksTable",
+                    createActionButton(inputId = "clust2peaksTable",
                                        label = "Send to Peak Table",
                                        icon = "share-from-square"))
            ),

components/mainpanel.R

@@ -1,7 +1,7 @@
 source("components/mainTab.R")
 source("components/qcTab.R")
 source("components/pcaTab.R")
-source("components/hcTab.R")
+source("components/clustTab.R")
 
 appMainPanel <- function(defaults) {
   m <- mainPanel(

components/pcaTab.R

@@ -45,11 +45,9 @@ pcaTab <- function() {
                                 multiple = FALSE,
                                 selected = defaults$pcaEllipse)),
              column(1,
-                    materialSwitch(
-                      inputId = "simpleLoadings",
-                      label = "Summarise loadings",
-                      value = defaults$simpleLoadings,
-                      status = "primary")
+                    checkboxInput(inputId = "simpleLoadings",
+                                  label = "Summarise loadings",
+                                  value = defaults$simpleLoadings)
              ),
              column(2,
                     createActionButton(inputId = "pca2peaksTable",