docs

R/LFQDataSummariser.R

@@ -16,6 +16,7 @@
 #' sum$hierarchy_counts_sample("wide")
 #' sum$hierarchy_counts_sample("long")
 #' sum$plot_hierarchy_counts_sample()
+#' sum$plot_hierarchy_counts_sample()
 #' tmp <- sum$interaction_missing_stats()
 #'
 #' sum$missingness_per_group()
@@ -44,16 +45,20 @@ LFQDataSummariser <- R6::R6Class(
     #' @description
     #' number of elements at each level in every sample
     #' @param value wide - wide format, long - long format, plot - ggplot
-    hierarchy_counts_sample = function(value=c("wide","long")){
+    #' @param nr_children get summary for 1,2 or more number of children
+    hierarchy_counts_sample = function(value=c("wide","long"), nr_children = 1){
       value <- match.arg(value)
-      fun <- prolfqua::hierarchy_counts_sample(self$lfq$data, self$lfq$config)
+      fun <- prolfqua::hierarchy_counts_sample(self$lfq$data, self$lfq$config,
+                                               nr_children = nr_children)
       return(fun(value))
     },
     #' @description
     #' barplot showing number of elements at each level in every sample
     #' @param value wide - wide format, long - long format, plot - ggplot
-    plot_hierarchy_counts_sample = function(){
-      fun <- prolfqua::hierarchy_counts_sample(self$lfq$data, self$lfq$config)
+    #' @param nr_children get summary for 1,2 or more number of children
+    plot_hierarchy_counts_sample = function(nr_children = 1){
+      fun <- prolfqua::hierarchy_counts_sample(self$lfq$data, self$lfq$config,
+                                               nr_children = nr_children)
       return(fun("plot"))
     },
     #' @description

R/tidyMS_R6_TransitionCorrelations.R

@@ -226,7 +226,7 @@ tidy_to_wide <- function(data,
 #' testthat::expect_equal(nrow(res$rowdata), nrow(res$data))
 #' testthat::expect_equal(ncol(res$data) - ncol(res$rowdata) , nrow(res$annotation))
 #' res <- tidy_to_wide_config(data, config, as.matrix = TRUE)
-#' stopifnot(all(dim(res$data) == c(28,  12))
+#' stopifnot(all(dim(res$data) == c(28,  12)))
 #' stopifnot(all(dim(res$annotation) == c(12,  4)))
 #' stopifnot(all(dim(res$rowdata) == c(28, 3)))
 #'

vignettes/SimulateData.Rmd

@@ -47,7 +47,7 @@ peptideAbundances <- prolfqua::sim_lfq_data(PEPTIDE = TRUE)
 library(prolfqua)
 
 atable <- AnalysisTableAnnotation$new()
-atable$sampleName = "sample"
+atable$fileName = "sample"
 atable$factors["group_"] = "group"
 atable$hierarchy[["protein_Id"]] = "proteinID"
 atable$hierarchy[["peptide_Id"]] = "peptideID"