Tidying code diablo_plot_tune

Plant-Food-Research-Open · Mar 12, 2024 · 95fe9e3 · 95fe9e3
1 parent 99e92cb
commit 95fe9e3
Showing 1 changed file with 31 additions and 11 deletions.
diff --git a/R/diablo.R b/R/diablo.R
@@ -432,11 +432,11 @@ diablo_tune <- function(mixomics_data, design_matrix, keepX_list = NULL, cpus =
 
 #' Plots DIABLO tune results
 #'
-#' Displays the error rate of a DIABLO run cross-validation to estimate the optimal number of features to retain from
-#' each dataset (\code{keepX}).
+#' Displays the error rate of a DIABLO run cross-validation to estimate the
+#' optimal number of features to retain from each dataset (\code{keepX}).
 #'
-#' @param tune_res The cross-validation results, computed with \code{\link{diablo_tune}}.
-#' @return A \code{ggplot2} object.
+#' @param tune_res The cross-validation results, computed with [diablo_tune()].
+#' @return A `ggplot2` object.
 #' @export
 diablo_plot_tune <- function(tune_res) {
   ## For devtools::check()
@@ -449,12 +449,17 @@ diablo_plot_tune <- function(tune_res) {
   error_label <- error_label[tune_res$measure]
   datasets_name <- names(tune_res$choice.keepX)
   comps <- colnames(tune_res$error.rate)
-  comps_colours <- RColorBrewer::brewer.pal(max(length(comps), 3), "Set2")[1:length(comps)]
+  comps_colours <- RColorBrewer::brewer.pal(max(length(comps), 3), "Set2")
+  comps_colours <- comps_colours[1:length(comps)]
   names(comps_colours) <- comps
 
   ## Reading error sd
-  if (is.null(rownames(tune_res$error.rate.sd))) rownames(tune_res$error.rate.sd) <- rownames(tune_res$error.rate)
-  if (is.null(colnames(tune_res$error.rate.sd))) colnames(tune_res$error.rate.sd) <- colnames(tune_res$error.rate)
+  if (is.null(rownames(tune_res$error.rate.sd))) {
+    rownames(tune_res$error.rate.sd) <- rownames(tune_res$error.rate)
+  }
+  if (is.null(colnames(tune_res$error.rate.sd))) {
+    colnames(tune_res$error.rate.sd) <- colnames(tune_res$error.rate)
+  }
 
   df_sd <- tibble::as_tibble(tune_res$error.rate.sd, rownames = "id") |>
     tidyr::pivot_longer(
@@ -471,7 +476,13 @@ diablo_plot_tune <- function(tune_res) {
       values_to = "error"
     ) |>
     dplyr::left_join(df_sd, by = c("id", "comp")) |>
-    tidyr::separate(id, into = datasets_name, sep = "_", remove = FALSE, convert = TRUE) |>
+    tidyr::separate(
+      id,
+      into = datasets_name,
+      sep = "_",
+      remove = FALSE,
+      convert = TRUE
+    ) |>
     dplyr::mutate(
       error_min = error - sd,
       error_max = error + sd
@@ -498,7 +509,10 @@ diablo_plot_tune <- function(tune_res) {
       ggplot2::ggplot(aes(x = dataset, y = id, fill = nb_retained_features)) +
       ggplot2::geom_tile() +
       ggplot2::scale_x_discrete(expand = c(0, 0)) +
-      ggplot2::scale_fill_viridis_c(option = "plasma", guide = ifelse(i == comps[1], "colourbar", "none")) +
+      ggplot2::scale_fill_viridis_c(
+        option = "plasma",
+        guide = ifelse(i == comps[1], "colourbar", "none")
+      ) +
       ggplot2::theme(
         axis.text.y = ggplot2::element_blank(),
         axis.ticks.y = ggplot2::element_blank(),
@@ -517,7 +531,9 @@ diablo_plot_tune <- function(tune_res) {
       ggplot2::ggplot(aes(x = id)) +
       ggplot2::geom_col(aes(y = error), fill = comps_colours[i], width = 1) +
       ggplot2::coord_flip() +
-      ggplot2::scale_y_continuous(expand = ggplot2::expansion(mult = c(0, 0.05))) +
+      ggplot2::scale_y_continuous(
+        expand = ggplot2::expansion(mult = c(0, 0.05))
+      ) +
       ggplot2::theme_bw() +
       ggplot2::theme(
         axis.text.y = ggplot2::element_blank(),
@@ -547,7 +563,11 @@ diablo_plot_tune <- function(tune_res) {
     if (i == comps[1]) common_legend <- ggpubr::get_legend(plot1)
   }
 
-  ggpubr::ggarrange(plotlist = plots_list, legend.grob = common_legend, legend = "bottom")
+  ggpubr::ggarrange(
+    plotlist = plots_list,
+    legend.grob = common_legend,
+    legend = "bottom"
+  )
 }
 
 #' Formatted table with optimal keepX values