vizualization adjustments

Author: ncborcherding

R/enrichItPlot.R

@@ -68,8 +68,7 @@ enrichItPlot <- function(res,
   if (plot.type == "bar") {                 
     p <- ggplot2::ggplot(res,
                          ggplot2::aes(x = .data[[x.measure]], y = .data$Term)) +
-      ggplot2::geom_col(fill = .colorizer(palette, n = 1), ...) +
-      ggplot2::facet_wrap(~ Database, scales = "free_y") +
+      ggplot2::geom_col(fill = .colorizer(palette, n = 1)) +
       ggplot2::labs(x = x.measure, y = NULL) +
       ggplot2::theme_classic()
 
@@ -80,19 +79,14 @@ enrichItPlot <- function(res,
         hjust = 0, size = 3)
     }
     p <- p + ggplot2::coord_cartesian(clip = "off")
-    return(patchwork::wrap_plots(p))
-  
   ## Dot Plot  
   } else if (plot.type == "dot") {         
-    if (!requireNamespace("patchwork", quietly = TRUE))
-      stop("Install 'patchwork' for facetted output.")
 
     p <- ggplot2::ggplot(res,
                          ggplot2::aes(x = .data$geneRatio, y = .data$Term,
                                       color = .data[[color.measure]],
                                       size   = .data$size*.data$geneRatio)) +
       ggplot2::geom_point(...) +
-      ggplot2::facet_wrap(~ Database, scales = "free_y") +
       ggplot2::scale_size_continuous(name = "Core Count") +
       ggplot2::labs(x = "geneRatio", y = NULL,
                     color = color.measure) +
@@ -101,8 +95,6 @@ enrichItPlot <- function(res,
 
     if (!is.null(palette))
       p <- p + ggplot2::scale_color_gradientn(colors = .colorizer(palette, 11))
-    return(patchwork::wrap_plots(p))
-  
   # Network Plot
   } else {                                  
     if (!requireNamespace("ggraph", quietly = TRUE))
@@ -126,7 +118,7 @@ enrichItPlot <- function(res,
     igraph::V(g)$type <- ifelse(igraph::V(g)$name %in% res$pathway, "pathway", "gene")
     igraph::V(g)$size <- ifelse(igraph::V(g)$type == "pathway", 8, 3)
 
-    ggraph::ggraph(g, layout = "fr") +
+    p <- ggraph::ggraph(g, layout = "fr") +
       ggraph::geom_edge_link(aes(alpha = after_stat(index)), show.legend = FALSE) +
       ggraph::geom_node_point(aes(size = .data$size,
                                   color = .data$type)) +
@@ -135,5 +127,8 @@ enrichItPlot <- function(res,
                              vjust = 1.5, check_overlap = TRUE) +
       ggplot2::scale_color_manual(values = .colorizer(palette, n = 2)) +
       ggplot2::theme_void()
+    
+    
   }
+  return(p)
 }

R/pcaEnrichment.R

@@ -140,9 +140,9 @@ pcaEnrichment <- function(input.data,
       ggplot2::geom_segment(data = loadings,
                             ggplot2::aes(x = 0, y = 0, xend = xend, yend = yend),
                             arrow = ggplot2::arrow(length = grid::unit(0.25, "cm"))) +
-      ggplot2::geom_text(data = loadings,
+      ggplot2::geom_label(data = loadings,
                          ggplot2::aes(x = xend, y = yend, label = names),
-                         size = 2, vjust = 1.1)
+                         size = 2)
   }
 
   g

R/ridgeEnrichment.R

@@ -123,7 +123,8 @@ ridgeEnrichment <- function(input.data,
     xlab(paste0(gene.set.use, "\nEnrichment Score")) +
     ggplot2::theme_classic(base_size = 11)
 
-  p <- .colorby(df, p, color.by, palette, type = "fill")
+  p <- .colorby(df, p, color.by, palette, type = "fill") + 
+    guides(fill = "none")
 
   ## facetting ------------------------------------------------------------
   if (!is.null(facet.by))

tests/testthat/test-enrichItPlot.R

@@ -1,7 +1,6 @@
 # test script for enrichItPlot.R - testcases are NOT comprehensive!
 
 skip_if_not_installed("fgsea")
-skip_if_not_installed("patchwork")       
 
 # helper data: run a very small fgsea ----------------------------------------
 set.seed(42)
@@ -31,20 +30,15 @@ res$Database <- ifelse(grepl("^DB1_", res$pathway), "DB1", "DB2")
 test_that("bar plot returns a patchwork object with ggplot inside", {
   plt <- enrichItPlot(res, plot.type = "bar", top = 3)
 
-  expect_s3_class(plt, "patchwork")
-  expect_true(inherits(plt[[1]], "ggplot"))
+  expect_true(inherits(plt, "ggplot"))
 })
 
 # ---------------------------------------------------------------------------
 # 2.  DOT plot ---------------------------------------------------------------
 test_that("dot plot returns a patchwork object and respects top argument", {
   plt <- enrichItPlot(res, plot.type = "dot", top = 1)
 
-  expect_s3_class(plt, "patchwork")
-  # only one term per database should survive top = 1
-  build <- ggplot2::ggplot_build(plt[[1]])
-  n_terms <- length(unique(build$data[[1]]$y))
-  expect_lte(n_terms, 2)          # 2 databases  ⇒ ≤2 rows in panel 1
+  expect_true(inherits(plt, "ggplot"))         
 })
 
 # ---------------------------------------------------------------------------