extend testing, improve handling of 1 per group

R/LFQDataStats.R

@@ -32,6 +32,7 @@
 #'
 #'
 #' lfqdata <- LFQData$new(bb$data, bb$config)
+#' # LFQDataStats$debug("violin")
 #' lfqstats <- lfqdata$get_Stats()
 #' stopifnot(ncol(lfqstats$stats_wide()) == 30)
 #' lfqstats$violin()
@@ -58,6 +59,17 @@
 #' stopifnot(ncol(lfqstats$stats_wide()) == 20)
 #' runallfuncs(lfqstats)
 #'
+#' # Group size 1
+#' bb <- prolfqua::sim_lfq_data_peptide_config(N=1)
+#' table_factors_size(bb$data,bb$config )
+#' lfqdata <- LFQData$new(bb$data, bb$config)
+#' # LFQDataStats$debug("initialize")
+#' lfqstats <- lfqdata$get_Stats()
+#'
+#' # stopifnot(ncol(lfqstats$stats_wide()) == 30)
+#' lfqstats$violin()
+#' runallfuncs(lfqstats)
+
 LFQDataStats <- R6::R6Class(
   "LFQDataStats",
   public = list(
@@ -78,7 +90,11 @@ LFQDataStats <- R6::R6Class(
 
       tb <- table_factors_size(lfqdata$data,lfqdata$config )
       if ( all(tb$n == 1) ) {
-        self$lfq$config$table$factorDepth <- self$lfq$config$table$factorDepth - 1
+        if(self$lfq$config$table$factorDepth > 1){
+          self$lfq$config$table$factorDepth <- self$lfq$config$table$factorDepth - 1
+        } else {
+          stats = "all"
+        }
       }
 
       if (stats == "interaction" ) {

R/simulate_LFQ_data.R

@@ -159,11 +159,11 @@ sim_lfq_data_peptide_config <- function(
     Nprot = 10,
     with_missing = TRUE,
     weight_missing = 0.2,
-    seed = 1234){
+    seed = 1234, N = 4){
   if (!is.null(seed)) {
     set.seed(seed)
   }
-  data <- sim_lfq_data(Nprot = Nprot, PEPTIDE = TRUE)
+  data <- sim_lfq_data(Nprot = Nprot, PEPTIDE = TRUE, N = N)
 
   not_missing <- !which_missing(data$abundance, weight_missing = weight_missing)
   # data <- data[not_missing,]

R/tidyMS_stats.R

@@ -173,7 +173,7 @@ poolvar <- function(res1, config,  method = c("V1","V2")){
 #' stopifnot(nrow(stats) == 20)
 #' stats <- summarize_stats(res2$data, res2$config, factor_key = NULL)
 #' stopifnot(nrow(stats) == 10)
-#'
+#' # TODO (WEW) add test when there is one level per group.
 summarize_stats <- function(pdata, config, factor_key = config$table$factor_keys_depth()){
   pdata <- complete_cases(pdata, config)
   intsym <- sym(config$table$get_response())
@@ -193,11 +193,11 @@ summarize_stats <- function(pdata, config, factor_key = config$table$factor_keys
   if (config$table$is_response_transformed == FALSE) {
     hierarchyFactor <- hierarchyFactor |> dplyr::mutate(CV = sd/meanAbundance * 100)
   }
-  if (is.null(factor_key)) {
+  if (is.null(factor_key) || length(factor_key) == 0) {
     hierarchyFactor <- dplyr::mutate(hierarchyFactor, !!config$table$factor_keys()[1] := "All")
   }
   hierarchyFactor <- ungroup(hierarchyFactor)
-  if (!is.null(factor_key)) {
+  if (length(factor_key) > 0 && !is.null(factor_key)) {
     hierarchyFactor <- prolfqua::make_interaction_column(hierarchyFactor, columns = factor_key, sep = ":")
   } else{
     hierarchyFactor$interaction <- "All"