move to simulated data in ContrastPlotter

R/ContrastsPlotter.R

@@ -5,14 +5,13 @@
 #' @family plotting
 #' @examples
 #'
-#' istar <- prolfqua_data('data_ionstar')$normalized()
-#' istar$config <- old2new(istar$config )
-#' istar_data <- dplyr::filter(istar$data ,protein_Id %in% sample(protein_Id, 100))
+#' istar <- sim_lfq_data_peptide_config()
 #' modelName <- "Model"
+#' head(istar$data)
 #' modelFunction <-
-#'   strategy_lmer("transformedIntensity  ~ dilution. + (1 | peptide_Id)",
+#'   strategy_lmer("abundance  ~ group_ + (1 | peptide_Id)",
 #'    model_name = modelName)
-#' pepIntensity <- istar_data
+#' pepIntensity <- istar$data
 #' config <- istar$config
 #' config$table$hierarchy_keys_depth()
 #' mod <- build_model(
@@ -23,10 +22,8 @@
 #'
 #'  #mod$get_coefficients()
 #'
-#'  Contr <- c("dil.b_vs_a" = "dilution.b - dilution.a",
-#'   "dil.e_vs_a" = "dilution.e - dilution.a"
-#'   ,"dil.e_vs_b" = "dilution.e - dilution.b",
-#'   "dil.c_vs_b" = "dilution.c - dilution.b"
+#'  Contr <- c("group_A_vs_Ctrl" = "group_A - group_Ctrl",
+#'  "group_B_vs_Ctrl" = "group_B - group_Ctrl"
 #'  )
 #' contrast <- prolfqua::Contrasts$new(mod,
 #'   Contr)
@@ -44,15 +41,14 @@
 #' volcano = list(list(score = "FDR", thresh = 0.1)),
 #' histogram = list(list(score = "p.value", xlim = c(0,1,0.05)),
 #'                  list(score = "FDR", xlim = c(0,1,0.05))),
-#'                  fcthresh = NULL,
+#'                  fcthresh = c(-1,1),
 #' score =list(list(score = "statistic", thresh = 5)))
 #' cp$fcthresh
 #' cp$volcano_plotly()
 #' p <- cp$score_plot(legend=FALSE)
 #' cp$score_plotly()
 #' p <- cp$histogram()
 #' p <- cp$histogram_estimate()
-#'
 #' res <- cp$volcano()
 #' respltly <- cp$volcano_plotly()
 #'
@@ -62,6 +58,7 @@
 #' names(res)
 #' cp$histogram_diff()
 #' cp$volcano()
+#'
 ContrastsPlotter <- R6::R6Class(
   "ContrastsPlotter",
   public = list(