Merge branch 'Modelling2R6' of https://github.com/wolski/prolfqua int…

…o Modelling2R6

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)

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)

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()))

R/utilities.R

@@ -460,12 +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, ...) {
-  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)
+  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) {