diff --git a/GATplots.R b/GATplots.R
index 7762ca8..8a1003d 100644
--- a/GATplots.R
+++ b/GATplots.R
@@ -6,9 +6,9 @@
 
 # Install -----------------------------------------------------------------
 
-if (!requireNamespace(c("ggplot2", "reshape2"), quietly = TRUE))
-  install.packages(c("ggplot2", "reshape2"), repos = "https://cloud.r-project.org")
-library(ggplot2)
+if (!requireNamespace(c("tidyverse", "reshape2"), quietly = TRUE))
+  install.packages(c("tidyverse", "reshape2"), repos = "https://cloud.r-project.org")
+library(tidyverse)
 library(reshape2)
 
 # Functions ---------------------------------------------------------------
@@ -31,12 +31,14 @@ gg_color_hue <- function(n) {
 GAT <- read.delim("Gat_CpG_hyper_hypo_results.tsv")
 
 # Nice names
-GAT$annotation <- as.character(GAT$annotation)
-GAT$annotation[GAT$annotation == "hg38_cpg_inter"] <- "Open Sea"
-GAT$annotation[GAT$annotation == "hg38_cpg_shelves"] <- "CpG Shelf"
-GAT$annotation[GAT$annotation == "hg38_cpg_islands"] <- "CpG Island"
-GAT$annotation[GAT$annotation == "hg38_cpg_shores"] <- "CpG Shore"
-GAT$annotation <- as.factor(GAT$annotation)
+GAT <- GAT %>%
+  dplyr::as_tibble() %>% 
+  dplyr::mutate(annotation = dplyr::recode_factor(annotation,
+                                                  "hg38_cpg_inter" = "Open Sea",
+                                                  "hg38_cpg_shelves" = "CpG Shelf",
+                                                  "hg38_cpg_islands" = "CpG Island",
+                                                  "hg38_cpg_shores" = "CpG Shore")
+                )
 
 GAT.1 <- GAT
 
@@ -46,7 +48,10 @@ GAT$fold[index] <- -(1/GAT$fold[index])
 
 # Order
 GAT <- dcast(GAT, annotation ~ track, value.var = "fold")
-order <- c("CpG Island", "CpG Shore", "CpG Shelf", "Open Sea")
+order <- c("CpG Island",
+           "CpG Shore",
+           "CpG Shelf",
+           "Open Sea")
 GAT$annotation <- factor(GAT$annotation,levels = order)
 GAT <- GAT[match(order, GAT$annotation),]
 row.names(GAT) <- c(1:nrow(GAT))
@@ -60,29 +65,53 @@ names(cols) <- order
 # Melt
 GAT <- melt(GAT)
 
-# Signifcance
+# Significance
 GAT.1 <- dcast(GAT.1, annotation ~ track, value.var = "qvalue")
-order <- c("CpG Island", "CpG Shore", "CpG Shelf", "Open Sea")
-GAT.1$annotation <- factor(GAT.1$annotation,levels = order)
+GAT.1$annotation <- factor(GAT.1$annotation, levels = order)
 GAT.1 <- GAT.1[match(order, GAT.1$annotation),]
 row.names(GAT.1) <- c(1:nrow(GAT.1))
 GAT.1$annotation <- factor(GAT.1$annotation, levels = rev(order))
 GAT.1 <- melt(GAT.1)
 GAT.1$signif <- ifelse(GAT.1$value < 0.05,1,0)
 GAT.1 <- GAT.1[-3]
-GAT <- merge(GAT, GAT.1, by =c("annotation", "variable"))
+GAT <- merge(GAT, GAT.1, by = c("annotation", "variable"))
 
 # Plot
-CpG <- ggplot(data = GAT, aes(annotation, y = value, fill = annotation)) +
-  geom_bar(stat = "identity") + coord_flip() + labs(y = "Fold Enrichment", x = element_blank()) + theme_classic() + 
-  theme(axis.text = element_text(size = 16), axis.title = element_text(size = 16),
-        strip.text = element_text(size = 16), legend.text = element_text(size = 14),
-        legend.title = element_text(size = 14)) +
-  scale_y_continuous(limits = c(-4,4), breaks = c(-4,-3,-2,-1,0,1,2,3,4)) +
-  scale_fill_manual(values = cols, breaks = order, name = "Annotation") + facet_grid(~variable) +
+CpG <- ggplot(data = GAT, aes(annotation,
+                              y = value,
+                              fill = annotation)
+              ) +
+  geom_bar(stat = "identity") +
+  coord_flip() +
+  labs(y = "Fold Enrichment",
+       x = element_blank()) +
+  theme_classic() + 
+  theme(axis.text = element_text(size = 16),
+        axis.title = element_text(size = 16),
+        strip.text = element_text(size = 16),
+        legend.text = element_text(size = 14),
+        legend.title = element_text(size = 14)
+        ) +
+  scale_y_continuous(limits = c(-4,4),
+                     breaks = c(-4,-3,-2,-1,0,1,2,3,4)
+                     ) +
+  scale_fill_manual(values = cols,
+                    breaks = order,
+                    name = "Annotation") +
+  facet_grid(~variable) +
   geom_hline(yintercept = 0) +
-  geom_text(data = GAT[(GAT$signif == 1 & GAT$value > 0), ], label = "*", size = 8, show.legend = FALSE, nudge_y = 0.5, nudge_x = -0.05) +
-  geom_text(data = GAT[(GAT$signif == 1 & GAT$value < 0), ], label = "*", size = 8, show.legend = FALSE, nudge_y = -0.5, nudge_x = -0.05)
+  geom_text(data = GAT[(GAT$signif == 1 & GAT$value > 0), ],
+            label = "*",
+            size = 8,
+            show.legend = FALSE,
+            nudge_y = 0.5,
+            nudge_x = -0.05) +
+  geom_text(data = GAT[(GAT$signif == 1 & GAT$value < 0), ],
+            label = "*",
+            size = 8,
+            show.legend = FALSE,
+            nudge_y = -0.5,
+            nudge_x = -0.05)
 
 ggsave("Gat_CpG_hyper_hypo.pdf",
        plot = CpG,
@@ -96,17 +125,19 @@ ggsave("Gat_CpG_hyper_hypo.pdf",
 GAT2 <- read.delim("Gat_genic_hyper_hypo_results.tsv")
 
 # Nice names
-GAT2$annotation <- as.character(GAT2$annotation)
-GAT2$annotation[GAT2$annotation == "enhancers_merged.bed"] <- "Enhancers"
-GAT2$annotation[GAT2$annotation == "intergenic_merged.bed"] <- "Intergenic"
-GAT2$annotation[GAT2$annotation == "introns_merged.bed"] <- "Intron"
-GAT2$annotation[GAT2$annotation == "onetofivekb_merged.bed"] <- "1-5 kb Upstream"
-GAT2$annotation[GAT2$annotation == "boundaries_merged.bed"] <- "Exon/Intron Boundaries"
-GAT2$annotation[GAT2$annotation == "threeUTRs_merged.bed"] <- "3' UTR"
-GAT2$annotation[GAT2$annotation == "exons_merged.bed"] <- "Exon"
-GAT2$annotation[GAT2$annotation == "fiveUTRs_merged.bed"] <- "5' UTR"
-GAT2$annotation[GAT2$annotation == "promoters_merged.bed"] <- "Promoter"
-GAT2$annotation <- as.factor(GAT2$annotation)
+GAT2 <- GAT2 %>%
+  dplyr::as_tibble() %>% 
+  dplyr::mutate(annotation = dplyr::recode_factor(annotation,
+                                                  "enhancers_merged.bed" = "Enhancers",
+                                                  "intergenic_merged.bed" = "Intergenic",
+                                                  "introns_merged.bed" = "Intron",
+                                                  "onetofivekb_merged.bed" = "1-5 kb Upstream",
+                                                  "boundaries_merged.bed" = "Exon/Intron Boundaries",
+                                                  "threeUTRs_merged.bed" = "3' UTR",
+                                                  "exons_merged.bed" = "Exon",
+                                                  "fiveUTRs_merged.bed" = "5' UTR",
+                                                  "promoters_merged.bed" = "Promoter")
+  )
 
 GAT2.1 <- GAT2
 
@@ -116,8 +147,16 @@ GAT2$fold[index1] <- -(1/GAT2$fold[index1])
 
 # Order
 GAT2 <- dcast(GAT2, annotation ~ track, value.var = "fold")
-order <- c("Enhancers", "1-5 kb Upstream", "Promoter", "5' UTR", "Exon", "Exon/Intron Boundaries", "Intron", "3' UTR", "Intergenic")
-GAT2$annotation <- factor(GAT2$annotation,levels=order)
+order <- c("Enhancers",
+           "1-5 kb Upstream",
+           "Promoter",
+           "5' UTR",
+           "Exon",
+           "Exon/Intron Boundaries",
+           "Intron",
+           "3' UTR",
+           "Intergenic")
+GAT2$annotation <- factor(GAT2$annotation, levels = order)
 GAT2 <- GAT2[match(order, GAT2$annotation),]
 row.names(GAT2) <- c(1:nrow(GAT2))
 GAT2$annotation <- factor(GAT2$annotation, levels = rev(order))
@@ -130,33 +169,57 @@ names(cols) <- order
 # Melt
 GAT2 <- melt(GAT2)
 
-# Signifcance
+# Significance
 GAT2.1 <- dcast(GAT2.1, annotation ~ track, value.var = "qvalue")
-order <- c("Enhancers", "1-5 kb Upstream", "Promoter", "5' UTR", "Exon", "Exon/Intron Boundaries", "Intron", "3' UTR", "Intergenic")
-GAT2.1$annotation <- factor(GAT2.1$annotation,levels=order)
+GAT2.1$annotation <- factor(GAT2.1$annotation,levels = order)
 GAT2.1 <- GAT2.1[match(order, GAT2.1$annotation),]
 row.names(GAT2.1) <- c(1:nrow(GAT2.1))
 GAT2.1$annotation <- factor(GAT2.1$annotation, levels = rev(order))
 GAT2.1 <- melt(GAT2.1)
 GAT2.1$signif <- ifelse(GAT2.1$value < 0.05,1,0)
 GAT2.1 <- GAT2.1[-3]
-GAT2 <- merge(GAT2, GAT2.1, by =c("annotation", "variable"))
+GAT2 <- merge(GAT2, GAT2.1, by = c("annotation", "variable"))
 
 # Plot
-gene <- ggplot(data=GAT2, aes(x=annotation, y =value, fill = annotation)) +
-  geom_bar(stat="identity") + coord_flip() + labs(y = "Fold Enrichment", x= element_blank()) + theme_classic() + 
-  theme(axis.text = element_text(size = 16), axis.title = element_text(size = 16),
-        strip.text = element_text(size = 16), legend.text = element_text(size = 14),
-        legend.title=element_text(size = 14)) +
-  scale_y_continuous(limits = c(-3.5,3.5), breaks = c(-3,-2,-1,0,1,2,3)) + 
-  scale_fill_manual(values = cols, breaks = order, name = "Annotation") + facet_grid(~variable) +
-  geom_hline(yintercept=0) +
-  geom_text(data = GAT2[(GAT2$signif ==1 & GAT2$value >0), ], label = "*", size=8, show.legend = FALSE, nudge_y = 0.5, nudge_x = -0.09) +
-  geom_text(data = GAT2[(GAT2$signif ==1 & GAT2$value <0), ], label = "*", size=8, show.legend = FALSE, nudge_y = -0.5, nudge_x = -0.09)
+gene <- ggplot(data = GAT2, aes(x = annotation,
+                                y = value,
+                                fill = annotation)
+               ) +
+  geom_bar(stat = "identity") +
+  coord_flip() +
+  labs(y = "Fold Enrichment",
+       x = element_blank()
+       ) +
+  theme_classic() + 
+  theme(axis.text = element_text(size = 16),
+        axis.title = element_text(size = 16),
+        strip.text = element_text(size = 16),
+        legend.text = element_text(size = 14),
+        legend.title = element_text(size = 14)
+        ) +
+  scale_y_continuous(limits = c(-3.5,3.5),
+                     breaks = c(-3,-2,-1,0,1,2,3)
+                     ) + 
+  scale_fill_manual(values = cols,
+                    breaks = order,
+                    name = "Annotation") +
+  facet_grid(~variable) +
+  geom_hline(yintercept = 0) +
+  geom_text(data = GAT2[(GAT2$signif ==1 & GAT2$value >0), ],
+            label = "*",
+            size = 8,
+            show.legend = FALSE,
+            nudge_y = 0.5,
+            nudge_x = -0.09) +
+  geom_text(data = GAT2[(GAT2$signif ==1 & GAT2$value <0), ],
+            label = "*",
+            size = 8,
+            show.legend = FALSE,
+            nudge_y = -0.5,
+            nudge_x = -0.09)
 
 ggsave("Gat_genic_hyper_hypo.pdf",
        plot = gene,
        device = NULL,
        width = 11,
        height = 6)
-