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Changed to tidyverse factor recoding and general tidying of plot script
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@ben-laufer
ben-laufer committed Feb 10, 2020
1 parent 032dd20 commit 8e6e8b1
Showing 1 changed file with 114 additions and 51 deletions.
165 changes: 114 additions & 51 deletions GATplots.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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 ---------------------------------------------------------------
Expand All @@ -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

Expand All @@ -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))
Expand All @@ -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,
Expand All @@ -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

Expand All @@ -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))
Expand All @@ -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)

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