Assorted fixes (#149)

* fix: strip ansi codes from error messages before displaying to user * feat: now automatically attempts to convert time to event variable to numeric before survival analysis and warns user
CCICB · Dec 7, 2023 · a75a071 · a75a071
1 parent 3dcf4dc
commit a75a071
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Showing 6 changed files with 36 additions and 12 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -162,6 +162,7 @@ Collate:
     'update_starting_maf_data_pool.R'
     'utils-pipe.R'
     'utils_bool_to_colour.R'
+    'utils_error_messages.R'
     'utils_installation.R'
     'utils_links.R'
     'utils_spacer.R'

diff --git a/R/mod_cnv.R b/R/mod_cnv.R
@@ -175,11 +175,11 @@ mod_cnv_server <- function(id, maf_data_pool){
             gistic_ <- TCGAgistic::tcga_gistic_load(cohort = cohort, source = source, cnLevel = cnLevel, verbose = FALSE)
           },
           error = function(err){
-            shinyWidgets::sendSweetAlert(session = session, title = "Failed to Read Gistic", text = tags$span(tags$code(as.character(err))))
+            shinyWidgets::sendSweetAlert(session = session, title = "Failed to Read Gistic", text = err2html(err))
             validate("Failed to Read Gistic")
           },
           warning = function(warn){
-            shinyWidgets::sendSweetAlert(session = session, title = "Failed to Read Gistic", text = tags$span(tags$code(as.character(warn))))
+            shinyWidgets::sendSweetAlert(session = session, title = "Failed to Read Gistic", text =  err2html(warn))
             validate("Failed to Read Gistic")
           }
 
@@ -197,11 +197,11 @@ mod_cnv_server <- function(id, maf_data_pool){
              shinyWidgets::sendSweetAlert(session = session, title = "Failed to Read Gistic", text = tags$span(tags$code("RDS file does not encode a GISTIC object.")))
          },
          error = function(err){
-           shinyWidgets::sendSweetAlert(session = session, title = "Failed to Read Gistic", text = tags$span(tags$code(as.character(err))))
+           shinyWidgets::sendSweetAlert(session = session, title = "Failed to Read Gistic", text = err2html(err))
            validate("Please supply a valid Gistic RDS")
          },
          warning = function(warn){
-           shinyWidgets::sendSweetAlert(session = session, title = "Failed to Read Gistic", text = tags$span(tags$code(as.character(warn))))
+           shinyWidgets::sendSweetAlert(session = session, title = "Failed to Read Gistic", text = err2html(warn))
            validate("Please supply a valid Gistic RDS")
          }
        ) 

diff --git a/R/mod_data_import.R b/R/mod_data_import.R
@@ -221,7 +221,9 @@ mod_data_import_server <- function(id, maf_data_pool) {
           session = session,
           title = paste0("Failed to Read Mutation File"),
           text = tags$div(
-            "Please ensure ",expected_mutation_filetype()," file/s ", message, "are formatted correctly.", tags$br(), tags$br(), tags$code(maf)
+            "Please ensure ",expected_mutation_filetype()," file/s ", message, "are formatted correctly.", 
+            tags$br(), tags$br(), 
+            err2html(maf)
           ),
           html = TRUE,
           type = "warning"

diff --git a/R/mod_mutational_signatures.R b/R/mod_mutational_signatures.R
@@ -105,7 +105,7 @@ mod_mutational_signatures_server <- function(id, maf_data_pool){
         shinyWidgets::sendSweetAlert(
           session = session, 
           title = "Failed to Read Mutalisk Input",
-          type = "error", text = tags$code(as.character(e))
+          type = "error", text = err2html(e) 
         )
         return(NULL)
       }

diff --git a/R/mod_survival_analysis.R b/R/mod_survival_analysis.R
@@ -102,8 +102,18 @@ mod_survival_analysis_server <- function(id, maf_data_pool){
       message('[1] Running maftools::survGroup')
       result = tryCatch(
         expr = { 
+
+          # In case selected 'time_to_event' column is non-numeric: convert to numeric and warn the user
+          mymaf = maf()
+          vec_time_to_event <- mymaf@clinical.data[[column_time_to_event()]]
+          mymaf@clinical.data[[column_time_to_event()]] <- as.numeric(vec_time_to_event)
+          if(!is.numeric(vec_time_to_event)){
+            shinyWidgets::sendSweetAlert(session = session, title = 'Incorrect type', text = 'The "Time to Event" column selected is non-numeric, please ensure you have the right column',type = 'warning')
+          }
+
+          # Perform Survival analysis
           maftools::survGroup(
-            maf = maf(), 
+            maf = mymaf, 
             top = input$in_num_genes_to_include, 
             geneSetSize = input$in_num_geneset_size, 
             minSamples = input$in_num_minsamples, 
@@ -143,11 +153,12 @@ mod_survival_analysis_server <- function(id, maf_data_pool){
 
 time_column_passes_sanitychecks <- function(column_name, clinical_dataframe){
   vec <- clinical_dataframe[[column_name]]
-
-  if(!is.numeric(vec))
-    return(FALSE)
-  else
-    return(TRUE)
+
+  return(TRUE)  
+  # if(!is.numeric(vec))
+  #   return(FALSE)
+  # else
+  #   return(TRUE)
 }
 
 

diff --git a/R/utils_error_messages.R b/R/utils_error_messages.R
@@ -0,0 +1,10 @@
+#' Format error messages as html
+#'
+#' @description Format error messages as html
+#'
+#' @return The return value, if any, from executing the utility.
+#'
+#' @noRd
+err2html <- function(err){
+  tags$code(HTML(cli::ansi_html(as.character(err))))
+}