[UPD] - new version of readQFeatures

UCLouvain-CBIO · Jul 11, 2024 · 151cf5f · 151cf5f
1 parent 5030820
commit 151cf5f
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Showing 6 changed files with 23 additions and 23 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -38,5 +38,5 @@ Suggests:
     rmarkdown,
     BiocStyle
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 VignetteBuilder: knitr
diff --git a/NAMESPACE b/NAMESPACE
@@ -8,6 +8,7 @@ importFrom(MultiAssayExperiment,getWithColData)
 importFrom(QFeatures,QFeatures)
 importFrom(QFeatures,addAssayLink)
 importFrom(QFeatures,filterFeatures)
+importFrom(QFeatures,readQFeatures)
 importFrom(QFeatures,zeroIsNA)
 importFrom(RColorBrewer,brewer.pal)
 importFrom(SummarizedExperiment,assay)
@@ -38,7 +39,6 @@ importFrom(plotly,layout)
 importFrom(plotly,plot_ly)
 importFrom(plotly,plotlyOutput)
 importFrom(plotly,renderPlotly)
-importFrom(scp,readSCP)
 importFrom(shiny,NS)
 importFrom(shiny,actionButton)
 importFrom(shiny,checkboxInput)

diff --git a/R/interface_import_tab.R b/R/interface_import_tab.R
@@ -14,7 +14,7 @@ import_tab <- function() {
         ),
         column(
             width = 6,
-            box_readscp_ui("readscp")
+            box_readqfeatures_ui("readqfeatures")
         )
     )
 }
diff --git a/R/interface_module_box_readscp.R → R/interface_module_box_readQFeatures.R b/R/interface_module_box_readscp.R → R/interface_module_box_readQFeatures.R
@@ -4,14 +4,14 @@
 #' @param id module id
 #'
 #' @return A shinydashboardPlus box object that contains the UI components to create an preview a QFeatures object
-#' @rdname INTERNAL_box_readscp_ui
+#' @rdname INTERNAL_box_readqfeatures_ui
 #' @keywords internal
 #'
 #' @importFrom shiny tagList selectInput checkboxInput actionButton downloadButton NS
 #' @importFrom shinydashboardPlus box
 #' @importFrom DT dataTableOutput
 #'
-box_readscp_ui <- function(id) {
+box_readqfeatures_ui <- function(id) {
     tagList(
         box(
             title = "QFeatures Converter",
@@ -35,13 +35,13 @@ box_readscp_ui <- function(id) {
                     style = "font-size: 14px;"
                 ),
                 selectInput(
-                    inputId = NS(id, "batch_col"),
-                    "Batch column :",
+                    inputId = NS(id, "run_col"),
+                    "Run/Batch column :",
                     choices = NULL
                 ),
                 selectInput(
-                    inputId = NS(id, "channel_col"),
-                    "Channel column :",
+                    inputId = NS(id, "quant_cols"),
+                    "Quantitative column :",
                     choices = NULL
                 ),
                 checkboxInput(
@@ -56,7 +56,7 @@ box_readscp_ui <- function(id) {
                 ),
                 checkboxInput(
                     inputId = NS(id, "singlecell"),
-                    label = "Single cell data",
+                    label = "Single cell data (WIP)",
                     value = FALSE
                 ),
                 actionButton(

diff --git a/R/server_import_tab.R b/R/server_import_tab.R
@@ -27,8 +27,8 @@ server_import_tab <- function(
         id = "sample",
         given_table = sample_table
     )
-    box_readscp_server(
-        "readscp",
+    box_readqfeatures_server(
+        "readqfeatures",
         imported_input,
         imported_sample
     )

diff --git a/R/server_module_box_readscp.R → R/server_module_box_readQFeatures.R b/R/server_module_box_readscp.R → R/server_module_box_readQFeatures.R
@@ -1,20 +1,20 @@
-#' A server module that contains the server logic to the readscp box module
+#' A server module that contains the server logic to the readQFeatures box module
 #'
 #' @param id module id
 #' @param input_table a reactiveVal containing the input table
 #' @param sample_table a reactiveVal containing the sample table
 #'
 #' @return A QFeatures object
-#' @rdname INTERNAL_box_readscp_server
+#' @rdname INTERNAL_box_readqfeatures_server
 #' @keywords internal
 #'
 #' @importFrom shiny is.reactive reactive moduleServer observe eventReactive updateSelectInput removeModal downloadHandler
 #' @importFrom DT renderDataTable datatable
-#' @importFrom scp readSCP
+#' @importFrom QFeatures readQFeatures
 #' @importFrom QFeatures zeroIsNA
 #' @importFrom SummarizedExperiment assay
 #'
-box_readscp_server <- function(id, input_table, sample_table) {
+box_readqfeatures_server <- function(id, input_table, sample_table) {
     stopifnot(is.reactive(input_table))
     stopifnot(is.reactive(sample_table))
 
@@ -24,13 +24,13 @@ box_readscp_server <- function(id, input_table, sample_table) {
                 "can be quite time consuming for large data sets",
                 sep = " "
             ))
+            print(typeof(unique(sample_table()[[input$quant_cols]])))
             global_rv$qfeatures <- error_handler(
-                scp::readSCP,
-                component_name = "QFeatures converting (readSCP)",
-                featureData = input_table(),
+                QFeatures::readQFeatures,
+                component_name = "QFeatures converting (readQFeatures)",
+                assayData = input_table(),
                 colData = sample_table(),
-                batchCol = input$batch_col,
-                channelCol = input$channel_col,
+                runCol = input$run_col,
                 removeEmptyCols = input$removeEmptyCols,
                 verbose = FALSE
             )
@@ -60,11 +60,11 @@ box_readscp_server <- function(id, input_table, sample_table) {
         observe({
             input$reload_button
             updateSelectInput(session,
-                "batch_col",
+                "run_col",
                 choices = colnames(sample_table())
             )
             updateSelectInput(session,
-                "channel_col",
+                "quant_cols",
                 choices = colnames(sample_table())
             )
         })