Bug Fix: ewce_plot with dendrogram

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: EWCE
 Type: Package
 Title: Expression Weighted Celltype Enrichment
-Version: 1.10.0
+Version: 1.10.1
 Authors@R:
     c(person(given = "Alan",
            family = "Murphy",

R/ewce_plot.r

@@ -23,7 +23,8 @@
 #' @inheritParams check_percent_hits 
 #'
 #' @returns A named list containing versions of the \link[ggplot2]{ggplot}
-#'  with and without the dendrogram. 
+#'  with and without the dendrogram. Note that cell type order on the x-axis is
+#'  based on hierarchical clustering for both plots if make_dendro = TRUE.   
 #'
 #' @export
 #' @import ggplot2
@@ -42,138 +43,146 @@ ewce_plot <- function(total_res,
                       heights = c(.3, 1), 
                       make_dendro = FALSE,
                       verbose = TRUE) {
-    # templateR:::args2vars(ewce_plot)
-
-    requireNamespace("ggplot2")
-    requireNamespace("patchwork")    
-
-    check_mtc_method(mtc_method = mtc_method)
-    multiList <- TRUE
-    if (is.null(total_res$list)) multiList <- FALSE
-    #### If using dendrogram ####
-    if(isTRUE(make_dendro)){
-        #### Check if ctd is provided ####
-        if(is.null(ctd)){
-            messager(
-                "Warning: Can only add the dendrogram when ctd is provided.",
-                "Setting make_dendro=FALSE.",
-                v=verbose)
-            make_dendro <- FALSE
-        } else {
-            # Find the relevant level of the CTD annotation 
-            if (length(ctd[[annotLevel]]$plotting) > 0) {
-                annotLevel <-
-                    which(unlist(lapply(ctd,
-                                        FUN = cells_in_ctd,
-                                        cells = as.character(
-                                            total_res$CellType
-                                        )
-                    )) == 1)
-                err_msg2 <- paste0(
-                    "All of the cells within total_res should come",
-                    " from a single annotation layer of the CTD"
-                )
-                if (length(annotLevel) == 0) {
-                    stop(err_msg2)
-                }
-            }
-            #### Set order of cells ####
-            if (length(ctd[[annotLevel]]$plotting) > 0) {
-                total_res$CellType <-
-                    factor(x = fix_celltype_names(total_res$CellType),
-                           levels = fix_celltype_names(
-                               ctd[[annotLevel]]$plotting$cell_ordering
-                           ), 
-                           ordered = TRUE
-                    )
-            }
-        } 
-    }
-    #### Multiple testing correction across all rows ####
-    if (!"q" %in% colnames(total_res)) {
-        total_res$q <- stats::p.adjust(total_res$p,
-            method = mtc_method
-        )
-    }
-    #### Mark significant rows with asterixes ####
-    ast_q <- rep("", dim(total_res)[1])
-    ast_q[total_res$q < q_threshold] <- "*"
-    total_res$ast_q <- ast_q
-    #### Plot ####
-    total_res$sd_from_mean[total_res$sd_from_mean < 0] <- 0
-    graph_theme <- ggplot2::theme_bw(base_size = 12, 
-                                     base_family = "Helvetica") +
-        ggplot2::theme(
-            text = ggplot2::element_text(size = 14),
-            axis.title.y = ggplot2::element_text(vjust = 0.6),
-            strip.background = ggplot2::element_rect(fill = "white"),
-            strip.text = ggplot2::element_text(color = "black")
-        )
-
-    upperLim <- max(abs(total_res$sd_from_mean), na.rm = TRUE)
-    total_res$y_ast <- total_res$sd_from_mean * 1.05
-    total_res$abs_sd <- abs(total_res$sd_from_mean)
-
-    if ("Direction" %in% colnames(total_res)) {
-        the_plot <- ggplot2::ggplot(total_res) +
-            ggplot2::geom_bar(
-                ggplot2::aes_string(x = "CellType", y = "abs_sd",
-                                    fill = "Direction"
-            ),
-            position = "dodge", stat = "identity"
-            ) +
-            graph_theme
+  # templateR:::args2vars(ewce_plot)
+
+  requireNamespace("ggplot2")
+  requireNamespace("patchwork")    
+
+  check_mtc_method(mtc_method = mtc_method)
+  multiList <- TRUE
+  if (is.null(total_res$list)) multiList <- FALSE
+  #### If using dendrogram ####
+  if(isTRUE(make_dendro)){
+    #### Check if ctd is provided ####
+    if(is.null(ctd)){
+      messager(
+        "Warning: Can only add the dendrogram when ctd is provided.",
+        "Setting make_dendro=FALSE.",
+        v=verbose)
+      make_dendro <- FALSE
     } else {
-        the_plot <- ggplot2::ggplot(total_res) +
-            ggplot2::geom_bar(
-                ggplot2::aes_string(x = "CellType", y = "abs_sd", 
-                                    fill = "abs_sd"),
-                stat = "identity"
-            ) +
-            ggplot2::scale_fill_gradient(low = "blue", high = "red") +
-            graph_theme +
-            ggplot2::theme(legend.position = "none")
-    }
-
-    # Setup the main plot
-    the_plot <- the_plot +
-        ggplot2::theme(
-            plot.margin = ggplot2::unit(c(.5, 0, 0, 0), "mm"),
-            axis.text.x = ggplot2::element_text(angle = 55, hjust = 1)
-        ) +
-        ggplot2::theme(panel.border = ggplot2::element_rect(
-            colour = "black",
-            fill = NA, linewidth = 1
-        )) +
-        ggplot2::xlab("Cell type") +
-        ggplot2::theme(strip.text.y = ggplot2::element_text(angle = 0)) +
-        ggplot2::ylab("Std.Devs. from the mean") 
-
-    the_plot <- the_plot +
-        ggplot2::scale_y_continuous(breaks = c(0, ceiling(upperLim * 0.66)),
-                                    expand = c(0, 1.1)) +
-        ggplot2::geom_text(
-            ggplot2::aes_string(label = "ast_q", x = "CellType", y = "y_ast"),
-            size = 10
+      # Find the relevant level of the CTD annotation 
+      if (length(ctd[[annotLevel]]$plotting) > 0) {
+        annotLevel <-
+          which(unlist(lapply(ctd,
+                              FUN = cells_in_ctd,
+                              cells = as.character(
+                                total_res$CellType
+                              )
+          )) == 1)
+        err_msg2 <- paste0(
+          "All of the cells within total_res should come",
+          " from a single annotation layer of the CTD"
         )
-    if (isTRUE(multiList)) {
-        the_plot <- the_plot +
-            ggplot2::facet_grid("list ~ .", 
-                                scales = "free", 
-                                space = "free_x")
-    }
-    #### Prepare output list ####
-    output <- list()
-    output$plain <- the_plot 
-    if (isTRUE(make_dendro)) {
+        if (length(annotLevel) == 0) {
+          stop(err_msg2)
+        }
+        cell_ordr <- ctd[[annotLevel]]$plotting$cell_ordering
+      }else{
+        #generate dendrogram - gives ordering
         ctdIN <- prep_dendro(ctdIN = ctd[[annotLevel]], 
                              expand = c(0, .66))  
-        output$withDendro <- patchwork::wrap_plots(
-            ctdIN$plotting$ggdendro_horizontal,
-            the_plot, 
-            heights = heights,
-            ncol = 1)
-    }
-
-    return(output)
-}
+        cell_ordr <- ctdIN$plotting$cell_ordering
+      }
+      #### Set order of cells ####
+      total_res$CellType <-
+        factor(x = fix_celltype_names(total_res$CellType),
+               levels = fix_celltype_names(
+                 cell_ordr
+               ), 
+               ordered = TRUE
+        )
+    } 
+  }
+  #### Multiple testing correction across all rows ####
+  if (!"q" %in% colnames(total_res)) {
+    total_res$q <- stats::p.adjust(total_res$p,
+                                   method = mtc_method
+    )
+  }
+  #### Mark significant rows with asterixes ####
+  ast_q <- rep("", dim(total_res)[1])
+  ast_q[total_res$q < q_threshold] <- "*"
+  total_res$ast_q <- ast_q
+  #### Plot ####
+  total_res$sd_from_mean[total_res$sd_from_mean < 0] <- 0
+  graph_theme <- ggplot2::theme_bw(base_size = 12, 
+                                   base_family = "Helvetica") +
+    ggplot2::theme(
+      text = ggplot2::element_text(size = 14),
+      axis.title.y = ggplot2::element_text(vjust = 0.6),
+      strip.background = ggplot2::element_rect(fill = "white"),
+      strip.text = ggplot2::element_text(color = "black")
+    )
+
+  upperLim <- max(abs(total_res$sd_from_mean), na.rm = TRUE)
+  total_res$y_ast <- total_res$sd_from_mean * 1.05
+  total_res$abs_sd <- abs(total_res$sd_from_mean)
+
+  if ("Direction" %in% colnames(total_res)) {
+    the_plot <- ggplot2::ggplot(total_res) +
+      ggplot2::geom_bar(
+        ggplot2::aes_string(x = "CellType", y = "abs_sd",
+                            fill = "Direction"
+        ),
+        position = "dodge", stat = "identity"
+      ) +
+      graph_theme
+  } else {
+    the_plot <- ggplot2::ggplot(total_res) +
+      ggplot2::geom_bar(
+        ggplot2::aes_string(x = "CellType", y = "abs_sd", 
+                            fill = "abs_sd"),
+        stat = "identity"
+      ) +
+      ggplot2::scale_fill_gradient(low = "blue", high = "red") +
+      graph_theme +
+      ggplot2::theme(legend.position = "none")
+  }
+
+  # Setup the main plot
+  the_plot <- the_plot +
+    ggplot2::theme(
+      plot.margin = ggplot2::unit(c(.5, 0, 0, 0), "mm"),
+      axis.text.x = ggplot2::element_text(angle = 55, hjust = 1)
+    ) +
+    ggplot2::theme(panel.border = ggplot2::element_rect(
+      colour = "black",
+      fill = NA, linewidth = 1
+    )) +
+    ggplot2::xlab("Cell type") +
+    ggplot2::theme(strip.text.y = ggplot2::element_text(angle = 0)) +
+    ggplot2::ylab("Std.Devs. from the mean") 
+
+  the_plot <- the_plot +
+    ggplot2::scale_y_continuous(breaks = c(0, ceiling(upperLim * 0.66)),
+                                expand = c(0, 1.1)) +
+    ggplot2::geom_text(
+      ggplot2::aes_string(label = "ast_q", x = "CellType", y = "y_ast"),
+      size = 10
+    )
+  if (isTRUE(multiList)) {
+    the_plot <- the_plot +
+      ggplot2::facet_grid("list ~ .", 
+                          scales = "free", 
+                          space = "free_x")
+  }
+  #### Prepare output list ####
+  output <- list()
+  output$plain <- the_plot 
+  if (isTRUE(make_dendro)) {
+    #ctdIN wion't exist if plotting found earlier
+    if(length(ctd[[annotLevel]]$plotting) > 0){
+      ctdIN <- prep_dendro(ctdIN = ctd[[annotLevel]], 
+                           expand = c(0, .66))  
+    }  
+    #update plot ordering by dendrogram
+    output$withDendro <- patchwork::wrap_plots(
+      ctdIN$plotting$ggdendro_horizontal,
+      the_plot, 
+      heights = heights,
+      ncol = 1)
+  }
+
+  return(output)
+}