fix broken plotting index

wilsoncai1992 · Feb 23, 2018 · fb64198 · fb64198
1 parent 208b919
commit fb64198
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Showing 2 changed files with 15 additions and 9 deletions.
diff --git a/R/utils.R b/R/utils.R
@@ -32,6 +32,8 @@ print.data_adapt <- function(x, ...) {
   print(get_composition(x, type = "small")[[1]])
 }
 
+################################################################################
+
 #' Method of \code{shinyprint} for objects of class \code{data_adapt}
 #'
 #' Provides HTML-based printing utility for examining data-adaptive statistics
@@ -71,6 +73,7 @@ shinyprint.data_adapt <- function(x) {
   ))
 }
 
+################################################################################
 
 #' Generic plot method for data_adapt class
 #'
@@ -99,39 +102,42 @@ plot.data_adapt <- function(x, ..., plot_type = c("biomarker", "adapt_param")) {
 
   mean_rank_top <- x$mean_rank_top
   prob_in_top <- x$prob_in_top
+
   n_top.want <- length(top_index)
 
   if ("biomarker" %in% plot_type) {
     # Plot sorted average CV-rank
     plot(
       mean_rank_top, ylab = "Mean CV-rank", pch = 20,
-      main = "Mean CV-rank of selected covariates \n (Smaller the better)"
+      main = "Mean CV-rank of selected covariates \n (smaller is better)"
     )
-
     calibrate::textxy(
-      (1:n_top.want) - 0.3, mean_rank_top + 0.5, top_index,
-      offset = .6
+      (seq_len(n_top.want)) - 0.3, mean_rank_top + 0.5, top_index,
+      offset = 0.6
     )
     abline(a = 0, b = 1, lty = 3)
   }
 
   if ("adapt_param" %in% plot_type) {
     # plot sorted q-values, labeled with index
-    temp.top_index <- c(1:n_top.want)[order(q_value)]
+    temp.top_index <- c(seq_len(n_top.want))[order(q_value)]
     plot(
       sort(q_value),
       pch = 20,
       ylab = "q-value",
-      main = "q-value of selected covariates \n (Smaller the better)"
+      main = "q-value of selected covariates \n (smaller is better)"
     )
     calibrate::textxy(
-      (1:n_top.want) - 0.3, sort(q_value), temp.top_index,
+      (seq_len(n_top.want))[seq_len(x$n_top)] - 0.3, sort(q_value),
+      temp.top_index,
       offset = 1
     )
     abline(h = 0.05, lty = 2)
   }
 }
 
+################################################################################
+
 #' Summary tables of the `adaptest` object
 #'
 #' @param object (data_adapt) object as returned by \code{adaptest}

diff --git a/vignettes/differentialExpression.Rmd b/vignettes/differentialExpression.Rmd
@@ -63,9 +63,9 @@ matrix. We demonstrate the necessary syntax for calling `adaptest` below:
 adaptest_out <- adaptest(Y = Y,
                          A = A,
                          W = NULL,
-                         n_top = 5,
+                         n_top = 25,
                          n_fold = 3,
-                         SL_lib = 'SL.glm',
+                         SL_lib = c("SL.glm", "SL.mean"),
                          parameter_wrapper = adaptest::rank_DE,
                          absolute = FALSE,
                          negative = FALSE)