[FEAT] - change table names

R/importQFeatures.R

@@ -7,8 +7,8 @@
 #' \item The first section (Import) of the app allow to convert tables to a QFeatures object.
 #' \item The second section (Pre-processing) of the app allow to perform some optional pre-processing steps.
 #' }
-#' @param sample_table A dataframe that contains the sample table.
-#' @param input_table A dataframe that contains the input table.
+#' @param colData A dataframe that contains the sample table.
+#' @param assayData A dataframe that contains the input table.
 #'
 #' @return Return the "importQFeatures" shiny app object.
 #' @export
@@ -19,14 +19,14 @@
 #'
 #' data("sampleTable")
 #' data("inputTable")
-#' app <- importQFeatures(sample_table = sampleTable, input_table = inputTable)
+#' app <- importQFeatures(colData = sampleTable, assayData = inputTable)
 #'
 #' if (interactive()) {
 #'     shiny::runApp(app)
 #' }
 #'
-importQFeatures <- function(sample_table = NULL, input_table = NULL) {
+importQFeatures <- function(colData = NULL, assayData = NULL) {
     ui <- build_ui()
-    server <- build_server(sample_table, input_table)
+    server <- build_server(colData, assayData)
     shinyApp(ui = ui, server = server)
 }

R/interface_module_box_read_table.R

@@ -13,11 +13,7 @@
 box_read_table_ui <- function(id) {
     tagList(
         box(
-            title = paste(
-                upper_first(id),
-                "Table",
-                sep = " "
-            ),
+            title = if (id == "input") "assayData" else "colData",
             status = "primary",
             width = 12,
             solidHeader = TRUE,

R/interface_module_qc_metrics.R

@@ -16,7 +16,7 @@ interface_module_qc_metrics <- function(id, type) {
             box(
                 title = "PCA",
                 status = "primary",
-                width = if (type == "features") 8 else 12,
+                width = 8,
                 solidHeader = FALSE,
                 collapsible = TRUE,
                 fluidRow(
@@ -48,16 +48,15 @@ interface_module_qc_metrics <- function(id, type) {
                     )
                 )
             ),
-            if (type == "features") {
-                box(
-                    title = "Single Feature Visualisation",
-                    status = "primary",
-                    width = 4,
-                    solidHeader = FALSE,
-                    collapsible = TRUE,
-                    interface_module_viz_box(NS(id, "viz_box"))
-                )
-            }
+
+            box(
+                title = "Single Feature Visualisation",
+                status = "primary",
+                width = 4,
+                solidHeader = FALSE,
+                collapsible = TRUE,
+                interface_module_viz_box(NS(id, "viz_box"))
+            )
         )
     )
 }

R/utils_global.R

@@ -627,8 +627,6 @@ features_boxplot <- function(assays_df) {
 #'
 
 unique_feature_boxplot <- function(assays_df, feature) {
-    print(head(assays_df))
-    print(feature)
     plot <- ggplot(assays_df[assays_df$feature_type == feature, , drop = FALSE], aes(x = sample_type, y = intensity, colour = sample_type)) +
         geom_boxplot()