From a79cd7b70d8a59ef9f0d99aa0ff6ebc1939f6a2c Mon Sep 17 00:00:00 2001
From: Witold Wolski <wewolski@gmail.com>
Date: Wed, 28 Aug 2024 15:03:35 +0200
Subject: [PATCH] limit factors key depth

---
 NAMESPACE                              |  1 +
 R/AnalysisConfiguration.R              | 52 +++++++++++++++++++++++++-
 R/LFQDataStats.R                       | 11 +++++-
 man/AnalysisConfiguration.Rd           |  3 +-
 man/AnalysisParameters.Rd              |  3 +-
 man/AnalysisTableAnnotation.Rd         |  3 +-
 man/INTERNAL_FUNCTIONS_BY_FAMILY.Rd    |  3 +-
 man/R6_extract_values.Rd               |  3 +-
 man/complete_cases.Rd                  |  3 +-
 man/concrete_AnalysisConfiguration.Rd  |  3 +-
 man/make_interaction_column.Rd         |  3 +-
 man/make_reduced_hierarchy_config.Rd   |  3 +-
 man/sample_subset.Rd                   |  3 +-
 man/separate_factors.Rd                |  3 +-
 man/separate_hierarchy.Rd              |  3 +-
 man/setup_analysis.Rd                  |  3 +-
 man/spread_response_by_IsotopeLabel.Rd |  3 +-
 man/table_factors.Rd                   | 36 +++++++++++++++++-
 man/table_factors_size.Rd              | 46 +++++++++++++++++++++++
 19 files changed, 170 insertions(+), 18 deletions(-)
 create mode 100644 man/table_factors_size.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 5f6f24733..34b1639f1 100644
--- 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
index 07b3befdc..d1c3ff5ff 100644
--- 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
index 08ff08ffc..195518ec3 100644
--- 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
index 88d9a5d79..0ef04ab9a 100644
--- a/man/AnalysisConfiguration.Rd
+++ b/man/AnalysisConfiguration.Rd
@@ -21,7 +21,8 @@ Other configuration:
 \code{\link{separate_hierarchy}()},
 \code{\link{setup_analysis}()},
 \code{\link{spread_response_by_IsotopeLabel}()},
-\code{\link{table_factors}()}
+\code{\link{table_factors}()},
+\code{\link{table_factors_size}()}
 }
 \concept{configuration}
 \section{Public fields}{
diff --git a/man/AnalysisParameters.Rd b/man/AnalysisParameters.Rd
index 2b1b8eea1..1399ac9ec 100644
--- a/man/AnalysisParameters.Rd
+++ b/man/AnalysisParameters.Rd
@@ -21,7 +21,8 @@ Other configuration:
 \code{\link{separate_hierarchy}()},
 \code{\link{setup_analysis}()},
 \code{\link{spread_response_by_IsotopeLabel}()},
-\code{\link{table_factors}()}
+\code{\link{table_factors}()},
+\code{\link{table_factors_size}()}
 }
 \concept{configuration}
 \section{Public fields}{
diff --git a/man/AnalysisTableAnnotation.Rd b/man/AnalysisTableAnnotation.Rd
index 4cc76154c..80f74e166 100644
--- a/man/AnalysisTableAnnotation.Rd
+++ b/man/AnalysisTableAnnotation.Rd
@@ -35,7 +35,8 @@ Other configuration:
 \code{\link{separate_hierarchy}()},
 \code{\link{setup_analysis}()},
 \code{\link{spread_response_by_IsotopeLabel}()},
-\code{\link{table_factors}()}
+\code{\link{table_factors}()},
+\code{\link{table_factors_size}()}
 }
 \concept{configuration}
 \section{Public fields}{
diff --git a/man/INTERNAL_FUNCTIONS_BY_FAMILY.Rd b/man/INTERNAL_FUNCTIONS_BY_FAMILY.Rd
index 3b556e650..54c3e664f 100644
--- a/man/INTERNAL_FUNCTIONS_BY_FAMILY.Rd
+++ b/man/INTERNAL_FUNCTIONS_BY_FAMILY.Rd
@@ -43,7 +43,8 @@ Other configuration:
 \code{\link{separate_hierarchy}()},
 \code{\link{setup_analysis}()},
 \code{\link{spread_response_by_IsotopeLabel}()},
-\code{\link{table_factors}()}
+\code{\link{table_factors}()},
+\code{\link{table_factors_size}()}
 
 Other deprecated: 
 \code{\link{intensity_summary_by_hkeys}()},
diff --git a/man/R6_extract_values.Rd b/man/R6_extract_values.Rd
index 1555d17ad..7117e81a0 100644
--- a/man/R6_extract_values.Rd
+++ b/man/R6_extract_values.Rd
@@ -27,7 +27,8 @@ Other configuration:
 \code{\link{separate_hierarchy}()},
 \code{\link{setup_analysis}()},
 \code{\link{spread_response_by_IsotopeLabel}()},
-\code{\link{table_factors}()}
+\code{\link{table_factors}()},
+\code{\link{table_factors_size}()}
 }
 \concept{configuration}
 \keyword{internal}
diff --git a/man/complete_cases.Rd b/man/complete_cases.Rd
index 634a6eab6..962689fe5 100644
--- a/man/complete_cases.Rd
+++ b/man/complete_cases.Rd
@@ -38,7 +38,8 @@ Other configuration:
 \code{\link{separate_hierarchy}()},
 \code{\link{setup_analysis}()},
 \code{\link{spread_response_by_IsotopeLabel}()},
-\code{\link{table_factors}()}
+\code{\link{table_factors}()},
+\code{\link{table_factors_size}()}
 }
 \concept{configuration}
 \keyword{internal}
diff --git a/man/concrete_AnalysisConfiguration.Rd b/man/concrete_AnalysisConfiguration.Rd
index 58cb02eb1..58695163f 100644
--- a/man/concrete_AnalysisConfiguration.Rd
+++ b/man/concrete_AnalysisConfiguration.Rd
@@ -71,6 +71,7 @@ Other configuration:
 \code{\link{separate_hierarchy}()},
 \code{\link{setup_analysis}()},
 \code{\link{spread_response_by_IsotopeLabel}()},
-\code{\link{table_factors}()}
+\code{\link{table_factors}()},
+\code{\link{table_factors_size}()}
 }
 \concept{configuration}
diff --git a/man/make_interaction_column.Rd b/man/make_interaction_column.Rd
index f51aa2eb9..f207e9b43 100644
--- a/man/make_interaction_column.Rd
+++ b/man/make_interaction_column.Rd
@@ -37,7 +37,8 @@ Other configuration:
 \code{\link{separate_hierarchy}()},
 \code{\link{setup_analysis}()},
 \code{\link{spread_response_by_IsotopeLabel}()},
-\code{\link{table_factors}()}
+\code{\link{table_factors}()},
+\code{\link{table_factors_size}()}
 }
 \concept{configuration}
 \keyword{internal}
diff --git a/man/make_reduced_hierarchy_config.Rd b/man/make_reduced_hierarchy_config.Rd
index d35f56296..983a9102d 100644
--- a/man/make_reduced_hierarchy_config.Rd
+++ b/man/make_reduced_hierarchy_config.Rd
@@ -43,7 +43,8 @@ Other configuration:
 \code{\link{separate_hierarchy}()},
 \code{\link{setup_analysis}()},
 \code{\link{spread_response_by_IsotopeLabel}()},
-\code{\link{table_factors}()}
+\code{\link{table_factors}()},
+\code{\link{table_factors_size}()}
 }
 \concept{configuration}
 \keyword{internal}
diff --git a/man/sample_subset.Rd b/man/sample_subset.Rd
index f94c4f624..945fcd807 100644
--- a/man/sample_subset.Rd
+++ b/man/sample_subset.Rd
@@ -31,7 +31,8 @@ Other configuration:
 \code{\link{separate_hierarchy}()},
 \code{\link{setup_analysis}()},
 \code{\link{spread_response_by_IsotopeLabel}()},
-\code{\link{table_factors}()}
+\code{\link{table_factors}()},
+\code{\link{table_factors_size}()}
 }
 \concept{configuration}
 \keyword{internal}
diff --git a/man/separate_factors.Rd b/man/separate_factors.Rd
index 357f4ebbd..904d93d16 100644
--- a/man/separate_factors.Rd
+++ b/man/separate_factors.Rd
@@ -36,7 +36,8 @@ Other configuration:
 \code{\link{separate_hierarchy}()},
 \code{\link{setup_analysis}()},
 \code{\link{spread_response_by_IsotopeLabel}()},
-\code{\link{table_factors}()}
+\code{\link{table_factors}()},
+\code{\link{table_factors_size}()}
 }
 \concept{configuration}
 \keyword{internal}
diff --git a/man/separate_hierarchy.Rd b/man/separate_hierarchy.Rd
index 21ccc5ed6..02ea4dc07 100644
--- a/man/separate_hierarchy.Rd
+++ b/man/separate_hierarchy.Rd
@@ -40,7 +40,8 @@ Other configuration:
 \code{\link{separate_factors}()},
 \code{\link{setup_analysis}()},
 \code{\link{spread_response_by_IsotopeLabel}()},
-\code{\link{table_factors}()}
+\code{\link{table_factors}()},
+\code{\link{table_factors_size}()}
 }
 \concept{configuration}
 \keyword{internal}
diff --git a/man/setup_analysis.Rd b/man/setup_analysis.Rd
index b22121606..86c488cfb 100644
--- a/man/setup_analysis.Rd
+++ b/man/setup_analysis.Rd
@@ -40,7 +40,8 @@ Other configuration:
 \code{\link{separate_factors}()},
 \code{\link{separate_hierarchy}()},
 \code{\link{spread_response_by_IsotopeLabel}()},
-\code{\link{table_factors}()}
+\code{\link{table_factors}()},
+\code{\link{table_factors_size}()}
 }
 \concept{configuration}
 \keyword{internal}
diff --git a/man/spread_response_by_IsotopeLabel.Rd b/man/spread_response_by_IsotopeLabel.Rd
index caa45311e..f8583742e 100644
--- a/man/spread_response_by_IsotopeLabel.Rd
+++ b/man/spread_response_by_IsotopeLabel.Rd
@@ -42,7 +42,8 @@ Other configuration:
 \code{\link{separate_factors}()},
 \code{\link{separate_hierarchy}()},
 \code{\link{setup_analysis}()},
-\code{\link{table_factors}()}
+\code{\link{table_factors}()},
+\code{\link{table_factors_size}()}
 }
 \concept{configuration}
 \keyword{internal}
diff --git a/man/table_factors.Rd b/man/table_factors.Rd
index f51243d6c..a750b9dad 100644
--- a/man/table_factors.Rd
+++ b/man/table_factors.Rd
@@ -4,6 +4,8 @@
 \alias{table_factors}
 \title{Table of distinct factors (sample annotation)}
 \usage{
+table_factors(pdata, configuration)
+
 table_factors(pdata, configuration)
 }
 \arguments{
@@ -12,11 +14,25 @@ table_factors(pdata, configuration)
 \item{config}{AnalysisConfiguration}
 }
 \description{
+Table of distinct factors (sample annotation)
+
 Table of distinct factors (sample annotation)
 }
 \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))
+
+
+
 istar <- sim_lfq_data_peptide_config()
 
 
@@ -43,7 +59,25 @@ Other configuration:
 \code{\link{separate_factors}()},
 \code{\link{separate_hierarchy}()},
 \code{\link{setup_analysis}()},
-\code{\link{spread_response_by_IsotopeLabel}()}
+\code{\link{spread_response_by_IsotopeLabel}()},
+\code{\link{table_factors_size}()}
+
+Other configuration: 
+\code{\link{AnalysisConfiguration}},
+\code{\link{AnalysisParameters}},
+\code{\link{AnalysisTableAnnotation}},
+\code{\link{INTERNAL_FUNCTIONS_BY_FAMILY}},
+\code{\link{R6_extract_values}()},
+\code{\link{complete_cases}()},
+\code{\link{concrete_AnalysisConfiguration}},
+\code{\link{make_interaction_column}()},
+\code{\link{make_reduced_hierarchy_config}()},
+\code{\link{sample_subset}()},
+\code{\link{separate_factors}()},
+\code{\link{separate_hierarchy}()},
+\code{\link{setup_analysis}()},
+\code{\link{spread_response_by_IsotopeLabel}()},
+\code{\link{table_factors_size}()}
 }
 \concept{configuration}
 \keyword{internal}
diff --git a/man/table_factors_size.Rd b/man/table_factors_size.Rd
new file mode 100644
index 000000000..539e5c8ed
--- /dev/null
+++ b/man/table_factors_size.Rd
@@ -0,0 +1,46 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/AnalysisConfiguration.R
+\name{table_factors_size}
+\alias{table_factors_size}
+\title{Table of distinct factors (sample annotation)}
+\usage{
+table_factors_size(pdata, configuration)
+}
+\arguments{
+\item{pdata}{data.frame}
+
+\item{config}{AnalysisConfiguration}
+}
+\description{
+Table of distinct factors (sample annotation)
+}
+\examples{
+
+
+istar <- sim_lfq_data_peptide_config()
+
+
+xx <- table_factors_size(istar$data,istar$config )
+stopifnot(all(xt$n == 4))
+
+}
+\seealso{
+Other configuration: 
+\code{\link{AnalysisConfiguration}},
+\code{\link{AnalysisParameters}},
+\code{\link{AnalysisTableAnnotation}},
+\code{\link{INTERNAL_FUNCTIONS_BY_FAMILY}},
+\code{\link{R6_extract_values}()},
+\code{\link{complete_cases}()},
+\code{\link{concrete_AnalysisConfiguration}},
+\code{\link{make_interaction_column}()},
+\code{\link{make_reduced_hierarchy_config}()},
+\code{\link{sample_subset}()},
+\code{\link{separate_factors}()},
+\code{\link{separate_hierarchy}()},
+\code{\link{setup_analysis}()},
+\code{\link{spread_response_by_IsotopeLabel}()},
+\code{\link{table_factors}()}
+}
+\concept{configuration}
+\keyword{internal}