limit factors key depth

fgcz · Aug 28, 2024 · a79cd7b · a79cd7b
1 parent 6e04309
commit a79cd7b
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Showing 19 changed files with 170 additions and 18 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -169,6 +169,7 @@ export(summarize_stats_quantiles)
 export(summary_ROPECA_median_p.scaled)
 export(table_facade)
 export(table_factors)
+export(table_factors_size)
 export(tidy_to_wide)
 export(tidy_to_wide_config)
 export(transform_work_intensity)

diff --git a/R/AnalysisConfiguration.R b/R/AnalysisConfiguration.R
@@ -329,12 +329,62 @@ sample_subset <- function(size, pdata, config){
 #' stopifnot(all(xt$n == 4))
 #'
 table_factors <- function(pdata, configuration){
-  factorsTab <- pdata |> dplyr::select(c(configuration$table$fileName, configuration$table$sampleName, configuration$table$factor_keys())) |>
+  factorsTab <- pdata |>
+    dplyr::select(c(configuration$table$fileName, configuration$table$sampleName, configuration$table$factor_keys())) |>
     dplyr::distinct() |>
     arrange(!!sym(configuration$table$sampleName))
   return(factorsTab)
 }
 
+#' Table of distinct factors (sample annotation)
+#' @param pdata data.frame
+#' @param config AnalysisConfiguration
+#'
+#' @export
+#' @keywords internal
+#' @family configuration
+#' @examples
+#'
+#'
+#' istar <- sim_lfq_data_peptide_config()
+#'
+#'
+#' xx <- table_factors(istar$data,istar$config )
+#' xx
+#' xt <- xx |> dplyr::group_by(!!!rlang::syms(istar$config$table$factor_keys())) |>
+#'  dplyr::summarize(n = dplyr::n())
+#' xt
+#' stopifnot(all(xt$n == 4))
+#'
+table_factors <- function(pdata, configuration){
+  factorsTab <- pdata |>
+    dplyr::select(c(configuration$table$fileName, configuration$table$sampleName, configuration$table$factor_keys())) |>
+    dplyr::distinct() |>
+    arrange(!!sym(configuration$table$sampleName))
+  return(factorsTab)
+}
+
+#' Table of distinct factors (sample annotation)
+#' @param pdata data.frame
+#' @param config AnalysisConfiguration
+#'
+#' @export
+#' @keywords internal
+#' @family configuration
+#' @examples
+#'
+#'
+#' istar <- sim_lfq_data_peptide_config()
+#'
+#'
+#' xx <- table_factors_size(istar$data,istar$config )
+#' stopifnot(all(xt$n == 4))
+#'
+table_factors_size <- function(pdata, configuration){
+  xx <- table_factors(pdata, configuration)
+  xx <- xx |> dplyr::group_by(dplyr::across(configuration$table$factor_keys_depth())) |> dplyr::summarize(n = dplyr::n())
+  return(xx)
+}
 
 # Functions - summarize hierarchies
 

diff --git a/R/LFQDataStats.R b/R/LFQDataStats.R
@@ -75,15 +75,22 @@ LFQDataStats <- R6::R6Class(
       stats <- match.arg(stats)
       self$lfq = lfqdata
       self$stat <- if (!self$lfq$is_transformed()) {"CV"} else {"sd"}
+
+      tb <- table_factors_size(lfqdata$data,lfqdata$config )
+      fd <- config$table$factor_keys_depth()
+      if ( all(tb$n == 1) ) {
+        fd <- head(fd, n = length(fd) - 1)
+      }
+
       if (stats == "interaction" ) {
-        self$statsdf <- prolfqua::summarize_stats(self$lfq$data, self$lfq$config)
+        self$statsdf <- prolfqua::summarize_stats(self$lfq$data, self$lfq$config, factor_key = fd)
       } else if (stats == "all" ) {
         self$statsdf <-
           prolfqua::summarize_stats_all(self$lfq$data, self$lfq$config)
       } else if (stats == "everything" ) {
 
         self$statsdf <- bind_rows(
-          prolfqua::summarize_stats(self$lfq$data, self$lfq$config),
+          prolfqua::summarize_stats(self$lfq$data, self$lfq$config, factor_key = fd),
           prolfqua::summarize_stats_all(self$lfq$data, self$lfq$config)
         )
       }

diff --git a/man/AnalysisConfiguration.Rd b/man/AnalysisConfiguration.Rd
diff --git a/man/AnalysisParameters.Rd b/man/AnalysisParameters.Rd
diff --git a/man/AnalysisTableAnnotation.Rd b/man/AnalysisTableAnnotation.Rd
diff --git a/man/INTERNAL_FUNCTIONS_BY_FAMILY.Rd b/man/INTERNAL_FUNCTIONS_BY_FAMILY.Rd
diff --git a/man/R6_extract_values.Rd b/man/R6_extract_values.Rd
diff --git a/man/complete_cases.Rd b/man/complete_cases.Rd
diff --git a/man/concrete_AnalysisConfiguration.Rd b/man/concrete_AnalysisConfiguration.Rd
diff --git a/man/make_interaction_column.Rd b/man/make_interaction_column.Rd
diff --git a/man/make_reduced_hierarchy_config.Rd b/man/make_reduced_hierarchy_config.Rd
diff --git a/man/sample_subset.Rd b/man/sample_subset.Rd
diff --git a/man/separate_factors.Rd b/man/separate_factors.Rd
diff --git a/man/separate_hierarchy.Rd b/man/separate_hierarchy.Rd
diff --git a/man/setup_analysis.Rd b/man/setup_analysis.Rd
diff --git a/man/spread_response_by_IsotopeLabel.Rd b/man/spread_response_by_IsotopeLabel.Rd
diff --git a/man/table_factors.Rd b/man/table_factors.Rd
diff --git a/man/table_factors_size.Rd b/man/table_factors_size.Rd