From 505f874c9a081625dc87eeaaf62cdf152554b8d4 Mon Sep 17 00:00:00 2001
From: wolski <wewolski@gmail.com>
Date: Tue, 3 Sep 2024 15:50:11 +0200
Subject: [PATCH 1/3] fix examples

---
 DESCRIPTION               | 2 +-
 R/AnalysisConfiguration.R | 2 +-
 man/table_factors_size.Rd | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 5c6d553b..557441a7 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -67,7 +67,7 @@ Suggests:
     SummarizedExperiment,
     proDA,
     vsn
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Roxygen: list(r6 = TRUE)
 Depends: 
     R (>= 4.1)
diff --git a/R/AnalysisConfiguration.R b/R/AnalysisConfiguration.R
index d1c3ff5f..fd57a0f9 100644
--- a/R/AnalysisConfiguration.R
+++ b/R/AnalysisConfiguration.R
@@ -378,7 +378,7 @@ table_factors <- function(pdata, configuration){
 #'
 #'
 #' xx <- table_factors_size(istar$data,istar$config )
-#' stopifnot(all(xt$n == 4))
+#' stopifnot(all(xx$n == 4))
 #'
 table_factors_size <- function(pdata, configuration){
   xx <- table_factors(pdata, configuration)
diff --git a/man/table_factors_size.Rd b/man/table_factors_size.Rd
index 539e5c8e..f2a461b7 100644
--- a/man/table_factors_size.Rd
+++ b/man/table_factors_size.Rd
@@ -21,7 +21,7 @@ istar <- sim_lfq_data_peptide_config()
 
 
 xx <- table_factors_size(istar$data,istar$config )
-stopifnot(all(xt$n == 4))
+stopifnot(all(xx$n == 4))
 
 }
 \seealso{

From dcb1333c96d0c7f755324e0db6876f355e041632 Mon Sep 17 00:00:00 2001
From: wolski <wewolski@gmail.com>
Date: Tue, 3 Sep 2024 22:13:33 +0200
Subject: [PATCH 2/3] fixo

---
 R/LFQDataPlotter.R | 2 +-
 R/utilities.R      | 5 -----
 2 files changed, 1 insertion(+), 6 deletions(-)

diff --git a/R/LFQDataPlotter.R b/R/LFQDataPlotter.R
index d75e2133..4350e2bc 100644
--- a/R/LFQDataPlotter.R
+++ b/R/LFQDataPlotter.R
@@ -12,13 +12,13 @@
 #'  istar$data,
 #'  istar$config)
 #' #LFQDataPlotter$debug("boxplots")
+#' LFQDataPlotter$debug("pairs_smooth")
 #' lfqplotter <- lfqdata$get_Plotter()
 #'
 #' stopifnot(class(lfqplotter$heatmap()) == "pheatmap")
 #' stopifnot(class(lfqplotter$heatmap_cor()) == "pheatmap")
 #' stopifnot("ggplot" %in% class(lfqplotter$pca()))
 #' stopifnot("plotly" %in%  class(lfqplotter$pca_plotly()))
-#'
 #' tmp <- lfqplotter$boxplots()
 #' stopifnot("ggplot" %in%  class(tmp$boxplot[[1]]))
 #' stopifnot("ggplot" %in% class(lfqplotter$missigness_histogram()))
diff --git a/R/utilities.R b/R/utilities.R
index 7f5db0a1..9dd74eb0 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -460,11 +460,6 @@ panel_cor <- function(x, y, digits = 2, ...)
 #' pairs_smooth(tmp,log="xy",main="small data", legend=TRUE)
 #' @seealso also \code{\link{pairs}}
 pairs_smooth <- function(data, legend = FALSE, ...) {
-  while (nrow(na.omit(data)) < 100) {
-    non_na_counts <- apply(data, 2, function(x) sum(!is.na(x)))
-    min_col <- which.min(non_na_counts)
-    data <- data[, -min_col, drop = FALSE]
-  }
 
   pairs(
     data,

From 019b0b55bfad3e62e56b3034a48b19ee1975c4e2 Mon Sep 17 00:00:00 2001
From: wolski <wewolski@gmail.com>
Date: Tue, 3 Sep 2024 22:33:32 +0200
Subject: [PATCH 3/3] temp

---
 R/utilities.R         | 6 +++++-
 man/LFQDataPlotter.Rd | 2 +-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/R/utilities.R b/R/utilities.R
index 9dd74eb0..502615fb 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -460,7 +460,11 @@ panel_cor <- function(x, y, digits = 2, ...)
 #' pairs_smooth(tmp,log="xy",main="small data", legend=TRUE)
 #' @seealso also \code{\link{pairs}}
 pairs_smooth <- function(data, legend = FALSE, ...) {
-
+  non_na_counts <- apply(data, 2, function(x) sum(!is.na(x)))
+  min_col <- which(non_na_counts < 2)
+  if(length(min_col) >= 1){
+    data <- data[, -min_col, drop = FALSE]
+  }
   pairs(
     data,
     upper.panel = function(x, y) {
diff --git a/man/LFQDataPlotter.Rd b/man/LFQDataPlotter.Rd
index 00fe9bdf..e3d890a6 100644
--- a/man/LFQDataPlotter.Rd
+++ b/man/LFQDataPlotter.Rd
@@ -19,13 +19,13 @@ lfqdata <- LFQData$new(
  istar$data,
  istar$config)
 #LFQDataPlotter$debug("boxplots")
+LFQDataPlotter$debug("pairs_smooth")
 lfqplotter <- lfqdata$get_Plotter()
 
 stopifnot(class(lfqplotter$heatmap()) == "pheatmap")
 stopifnot(class(lfqplotter$heatmap_cor()) == "pheatmap")
 stopifnot("ggplot" \%in\% class(lfqplotter$pca()))
 stopifnot("plotly" \%in\%  class(lfqplotter$pca_plotly()))
-
 tmp <- lfqplotter$boxplots()
 stopifnot("ggplot" \%in\%  class(tmp$boxplot[[1]]))
 stopifnot("ggplot" \%in\% class(lfqplotter$missigness_histogram()))