Merge pull request #27 from itrujnara/bug_fixes

Added light mode plots

bin/plot_orthologs.R

@@ -16,10 +16,22 @@ if (length(args) < 2) {
 }
 
 # Styles
-text_color <- "#DDDDDD"
+text_color_darkmode <- "#DDDDDD"
+text_color_lightmode <- "#333333"
 bg_color <- "transparent"
 font_size <- 16
 
+customize_theme <- function(font_size, text_color, bg_color) {
+    theme(legend.position = "right",
+        text = element_text(size = font_size, color = text_color),
+        axis.text = element_text(size = font_size, color = text_color),
+        panel.grid = element_line(color = text_color),
+        plot.background = element_rect(color = bg_color, fill = bg_color),
+        panel.background = element_rect(color = bg_color, fill = bg_color))
+}
+
+theme_dark <- customize_theme(font_size, text_color_darkmode, bg_color)
+theme_light <- customize_theme(font_size, text_color_lightmode, bg_color)
 # Load the data
 data <- read.csv(args[1], header = TRUE, stringsAsFactors = FALSE)
 
@@ -35,33 +47,39 @@ crosstable <- dcast(melted_data, method ~ score)
 melted_crosstable <- melt(crosstable, id.vars = "method", variable.name = "score", value.name = "count")
 
 # Plot the data
-p <- ggplot(melted_crosstable, aes(x = method, y = count, fill = score)) +
+supports <- ggplot(melted_crosstable, aes(x = method, y = count, fill = score)) +
     geom_bar(stat = "identity", position = "stack") +
     theme_minimal() +
     theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
     labs(title = "Support for predictions", x = "Database", y = "Number of orthologs", fill = "Support") +
-    scale_fill_manual(values = c("#59B4C3", "#74E291", "#8F7AC2", "#EFF396", "#FF9A8D")) +
-    theme(legend.position = "right",
-        text = element_text(size = font_size, color = text_color),
-        axis.text.x = element_text(size = font_size, color = text_color),
-        axis.text.y = element_text(size = font_size, color = text_color),
-        plot.background = element_rect(color = bg_color, fill = bg_color),
-        panel.background = element_rect(color = bg_color, fill = bg_color))
+    scale_fill_manual(values = c("#59B4C3", "#74E291", "#8F7AC2", "#EFF396", "#FF9A8D"))
+
+supports_dark <- supports + theme_dark
 
-ggsave(paste0(args[2], "_supports.png"), plot = p, width = 6, height = 10, dpi = 300)
+ggsave(paste0(args[2], "_supports_dark.png"), plot = supports_dark, width = 6, height = 10, dpi = 300)
+
+supports_light <- supports + theme_light
+
+ggsave(paste0(args[2], "_supports_light.png"), plot = supports_light, width = 6, height = 10, dpi = 300)
 
 # Make a Venn diagram
 venn.data <- list()
 for (i in colnames(data)[4:ncol(data)-1]) {
     hits <- (data %>% filter(data[, i] == 1) %>% select(id))$id
     venn.data[[i]] <- hits
 }
-venn.plot <- ggVennDiagram(venn.data, set_color = text_color) +
-    theme(legend.position = "none",
-        text = element_text(size = font_size, color = text_color),
-        plot.background = element_rect(color = bg_color, fill = bg_color),
-        panel.background = element_rect(color = bg_color, fill = bg_color))
-ggsave(paste0(args[2], "_venn.png"), plot = venn.plot, width = 6, height = 6, dpi = 300)
+
+venn_plot_dark <- ggVennDiagram(venn.data, set_color = text_color_darkmode) +
+    theme_dark +
+    theme(panel.grid = element_blank(), axis.text = element_text(color = "transparent"), legend.position = "none")
+
+ggsave(paste0(args[2], "_venn_dark.png"), plot = venn_plot_dark, width = 6, height = 6, dpi = 300)
+
+venn_plot_light <- ggVennDiagram(venn.data, set_color = text_color_lightmode) +
+    theme_light +
+    theme(panel.grid = element_blank(), axis.text = element_text(color = "transparent"), legend.position = "none")
+
+ggsave(paste0(args[2], "_venn_light.png"), plot = venn_plot_light, width = 6, height = 6, dpi = 300)
 
 # Make a plot with Jaccard index for each pair of methods
 jaccard <- data.frame(method1 = character(), method2 = character(), jaccard = numeric())
@@ -77,18 +95,19 @@ for (i in 4:ncol(data)-1) {
         jaccard <- rbind(jaccard, data.frame(method1 = method1, method2 = method2, jaccard = length(intersect(hits1, hits2)) / length(union(hits1, hits2))))
     }
 }
-p <- ggplot(jaccard, aes(x = method1, y = method2, fill = jaccard)) +
+
+jaccard_plot <- ggplot(jaccard, aes(x = method1, y = method2, fill = jaccard)) +
     geom_tile() +
     geom_text(aes(label = round(jaccard, 2)), size=5) +
     scale_fill_gradient(low = "#59B4C3", high = "#EFF396") +
     theme_minimal() +
     theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
-    labs(title = "Jaccard Index", x = "", y = "", fill = "Jaccard Index") +
-    theme(legend.position = "right",
-        text = element_text(size = font_size, color = text_color),
-        axis.text.x = element_text(size = font_size, color = text_color),
-        axis.text.y = element_text(size = font_size, color = text_color),
-        plot.background = element_rect(color = bg_color, fill = bg_color),
-        panel.background = element_rect(color = bg_color, fill = bg_color))
+    labs(x = "", y = "", fill = "Jaccard Index")
+
+jaccard_plot_dark <- jaccard_plot + theme_dark
+
+ggsave(paste0(args[2], "_jaccard_dark.png"), plot = jaccard_plot_dark, width = 6, height = 6, dpi = 300)
+
+jaccard_plot_light <- jaccard_plot + theme_light
 
-ggsave(paste0(args[2], "_jaccard.png"), plot = p, width = 6, height = 6, dpi = 300)
+ggsave(paste0(args[2], "_jaccard_light.png"), plot = jaccard_plot_light, width = 6, height = 6, dpi = 300)

bin/plot_tree.R

@@ -7,7 +7,8 @@ library(treeio)
 library(ggtree)
 library(ggplot2)
 
-fgcolor <- "#eeeeee"
+fgcolor_dark <- "#dddddd"
+fgcolor_light <- "#333333"
 bgcolor <- "transparent"
 
 args <- commandArgs(trailingOnly = TRUE)
@@ -17,8 +18,17 @@ if (length(args) < 3) {
 }
 
 tree <- read.tree(args[1])
-p <- ggtree(tree, color = fgcolor) +
-    geom_tiplab(color = fgcolor) +
+
+p_dark <- ggtree(tree, color = fgcolor_dark) +
+    geom_tiplab(color = fgcolor_dark) +
+    theme_tree() +
+    theme(panel.background = element_rect(color = bgcolor, fill = bgcolor), plot.background = element_rect(color = bgcolor, fill = bgcolor))
+
+ggsave(paste0(args[2], "_", args[3], "_tree_dark.png"), dpi = 300, height = 16, width = 8)
+
+p_light <- ggtree(tree, color = fgcolor_light) +
+    geom_tiplab(color = fgcolor_light) +
     theme_tree() +
     theme(panel.background = element_rect(color = bgcolor, fill = bgcolor), plot.background = element_rect(color = bgcolor, fill = bgcolor))
-ggsave(paste0(args[2], "_", args[3], "_tree.png"), dpi = 300, height = 16, width = 8)
+
+ggsave(paste0(args[2], "_", args[3], "_tree_light.png"), dpi = 300, height = 16, width = 8)

modules/local/plot_orthologs.nf

@@ -10,10 +10,10 @@ process PLOT_ORTHOLOGS {
     tuple val(meta), path(score_table)
 
     output:
-    tuple val(meta), path("*_supports.png") , emit: supports
-    tuple val(meta), path("*_venn.png")     , emit: venn
-    tuple val(meta), path("*_jaccard.png")  , emit: jaccard
-    path "versions.yml"                     , emit: versions
+    tuple val(meta), path("*_supports_light.png"), path("*_supports_dark.png"), emit: supports
+    tuple val(meta), path("*_venn_light.png"), path("*_venn_dark.png")        , emit: venn
+    tuple val(meta), path("*_jaccard_light.png"), path("*_jaccard_dark.png")  , emit: jaccard
+    path "versions.yml"                          , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -32,9 +32,12 @@ process PLOT_ORTHOLOGS {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}_supports.png
-    touch ${prefix}_venn.png
-    touch ${prefix}_jaccard.png
+    touch ${prefix}_supports_dark.png
+    touch ${prefix}_supports_light.png
+    touch ${prefix}_venn_dark.png
+    touch ${prefix}_venn_light.png
+    touch ${prefix}_jaccard_dark.png
+    touch ${prefix}_jaccard_light.png
 
     cat <<- END_VERSIONS > versions.yml
     "${task.process}":

modules/local/plot_tree.nf

@@ -11,8 +11,8 @@ process PLOT_TREE {
     val method
 
     output:
-    tuple val(meta), path("*.png"), emit: plot
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path("*_light.png"), path("*_dark.png") , emit: plot
+    path "versions.yml"                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -31,7 +31,8 @@ process PLOT_TREE {
     stub:
     prefix = task.ext.prefix ?: meta.id
     """
-    touch ${prefix}_${method}_tree.png
+    touch ${prefix}_${method}_tree_dark.png
+    touch ${prefix}_${method}_tree_light.png
 
     cat <<- END_VERSIONS > versions.yml
     "${task.process}":

workflows/reportho.nf

@@ -94,8 +94,8 @@ workflow REPORTHO {
             ALIGN.out.alignment
         )
 
-        ch_iqtree = MAKE_TREES.out.mlplot
-        ch_fastme = MAKE_TREES.out.meplot
+        ch_iqtree = MAKE_TREES.out.mlplot.map { [it[0], it[1]] }
+        ch_fastme = MAKE_TREES.out.meplot.map { [it[0], it[1]] }
 
         ch_versions = ch_versions.mix(MAKE_TREES.out.versions)
     }
@@ -111,9 +111,9 @@ workflow REPORTHO {
             GET_ORTHOLOGS.out.seqinfo,
             GET_ORTHOLOGS.out.score_table,
             GET_ORTHOLOGS.out.orthologs,
-            GET_ORTHOLOGS.out.supports_plot,
-            GET_ORTHOLOGS.out.venn_plot,
-            GET_ORTHOLOGS.out.jaccard_plot,
+            GET_ORTHOLOGS.out.supports_plot.map { [it[0], it[1]]},
+            GET_ORTHOLOGS.out.venn_plot.map { [it[0], it[1]]},
+            GET_ORTHOLOGS.out.jaccard_plot.map { [it[0], it[1]]},
             GET_ORTHOLOGS.out.stats,
             ch_seqhits,
             ch_seqmisses,