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Fig_RT_domain_plots.Rmd
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---
title: "RT_Domain_analysis"
author: "Weiyan"
date: "1/8/2019"
output: github_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
# 1. Load data and data clean
```{r}
setwd("/Users/weiyanjia/Desktop/Randal S. Tibbetts/FUS project/Bioinfo_analysis/RT_Domain_identification_analysis/Anotation_results")
library(rtracklayer)
import ("U2OS_segway.bed", format = "bed")
U2OS_segway<- read.delim("U2OS_segway.bed", header = FALSE, sep ="\t", stringsAsFactors = FALSE)
Clone110_segway<- read.delim("Clone110_segway.bed", header = FALSE, sep ="\t", stringsAsFactors = FALSE)
FUSClone110_segway<- read.delim("FUSClone110_segway.bed", header = FALSE, sep ="\t", stringsAsFactors = FALSE)
FUSClone110_segway_backup <- FUSClone110_segway
head(FUSClone110_segway)
FUSClone110_segway$domain[FUSClone110_segway$V4 == 1 ]<- 0
FUSClone110_segway$domain[FUSClone110_segway$V4 == 0 ]<- 2
FUSClone110_segway$domain[FUSClone110_segway$V4 == 2 ]<- 1
FUSClone110_segway$color[FUSClone110_segway$domain == 1 ]<- "217,95,2"
FUSClone110_segway$color[FUSClone110_segway$domain == 0 ]<- "27,158,119"
FUSClone110_segway$color[FUSClone110_segway$domain == 2 ]<- "117,112,179"
FUSClone110_segway$V4 <- FUSClone110_segway$domain
FUSClone110_segway$V9 <- FUSClone110_segway$color
FUSClone110_segway$domain <- NULL
FUSClone110_segway$color <- NULL
# write.table(FUSClone110_segway,"FUSClone110_segway_x.bed", sep="\t", row.names=FALSE, quote=FALSE, col.names = FALSE)
# _v2 with label
U2OS_segway_v2 <- U2OS_segway
Clone110_segway_v2 <- Clone110_segway
FUSClone110_segway_v2 <- FUSClone110_segway
U2OS_segway_v2$domain[U2OS_segway_v2$V4 == 0 ]<- "E"
U2OS_segway_v2$domain[U2OS_segway_v2$V4 == 1 ]<- "L"
U2OS_segway_v2$domain[U2OS_segway_v2$V4 == 2 ]<- "M"
Clone110_segway_v2$domain[Clone110_segway_v2$V4 == 0 ]<- "E"
Clone110_segway_v2$domain[Clone110_segway_v2$V4 == 1 ]<- "L"
Clone110_segway_v2$domain[Clone110_segway_v2$V4 == 2 ]<- "M"
FUSClone110_segway_v2$domain[FUSClone110_segway_v2$V4 == 0 ]<- "E"
FUSClone110_segway_v2$domain[FUSClone110_segway_v2$V4 == 1 ]<- "L"
FUSClone110_segway_v2$domain[FUSClone110_segway_v2$V4 == 2 ]<- "M"
# rename columns
library(plyr)
U2OS_segway_v2 <- rename(U2OS_segway_v2,c('V1'='chr', 'V2'='star','V3'='end'))
U2OS_segway_v2$domain_size <- U2OS_segway_v2$end - U2OS_segway_v2$star
U2OS_segway_v2$sample <- "U2OS"
Clone110_segway_v2 <- rename(Clone110_segway_v2,c('V1'='chr', 'V2'='star','V3'='end'))
Clone110_segway_v2$domain_size <- Clone110_segway_v2$end - Clone110_segway_v2$star
Clone110_segway_v2$sample <- "Clone110"
FUSClone110_segway_v2 <- rename(FUSClone110_segway_v2,c('V1'='chr', 'V2'='star','V3'='end'))
FUSClone110_segway_v2$domain_size <- FUSClone110_segway_v2$end - FUSClone110_segway_v2$star
FUSClone110_segway_v2$sample <- "FUSClone110"
sub_U2OS_segway_v2 <- subset(U2OS_segway_v2, select=c("domain", "domain_size","sample"))
sub_Clone110_segway_v2 <- subset(Clone110_segway_v2, select=c("domain", "domain_size","sample"))
sub_FUSClone110_segway_v2 <- subset(FUSClone110_segway_v2, select=c("domain", "domain_size","sample"))
all_sample_segway_v2 = rbind(sub_U2OS_segway_v2, sub_Clone110_segway_v2,sub_FUSClone110_segway_v2)
all_sample_segway_v2$domain <- factor(all_sample_segway_v2$domain, levels= c("E","M","L"))
all_sample_segway_v2$sample <- factor(all_sample_segway_v2$sample, levels= c("U2OS","Clone110","FUSClone110"))
all_sample_segway_v2$domain_size <- sapply(all_sample_segway_v2$domain_size, as.numeric)
U2OS_segway_v2$domain_size <- sapply(U2OS_segway_v2$domain_size, as.numeric)
Clone110_segway_v2$domain_size <- sapply(Clone110_segway_v2$domain_size, as.numeric)
FUSClone110_segway_v2$domain_size <- sapply(FUSClone110_segway_v2$domain_size, as.numeric)
# write.table(U2OS_segway_v2,"U2OS_segway_v2.txt", sep="\t", row.names=FALSE, quote=FALSE, col.names = TRUE)
# write.table(Clone110_segway_v2,"Clone110_segway_v2.txt", sep="\t", row.names=FALSE, quote=FALSE, col.names = TRUE)
# write.table(FUSClone110_segway_v2,"FUSClone110_segway_v2.txt", sep="\t", row.names=FALSE, quote=FALSE, col.names = TRUE)
# write.table(all_sample_segway_v2,"all_sample_segway_v2.txt", sep="\t", row.names=FALSE, quote=FALSE, col.names = TRUE)
# U2OS_segway_v2
# Clone110_segway_v2
# FUSClone110_segway_v2
# all_sample_segway_v2
```
# 2. Domain size distribution
## 2.1 boxplot of domain size
```{r fig.height=6, fig.width=8}
library(ggpubr)
all_sample_segway_v2 <- all_sample_segway_v2%>%
tidyr::drop_na()
my_comparisons <- list(c("U2OS", "Clone110"), c("U2OS", "FUSClone110"))
ggboxplot(all_sample_segway_v2, x = "sample",
y = "domain_size",
facet.by = "domain",
short.panel.labs = TRUE,
legend.title ="",
x.text.angle = 45,
#repel = TRUE,
#combine = TRUE,
#merge = TRUE,
xlab ="Replication Domain",
ylab = "Domain Size (bp)",
color = "sample",
palette = "aaas"
)+
yscale("log10", .format = TRUE)+
stat_compare_means(comparisons = my_comparisons, aes(label = paste0("p = ", ..p.format..)),
method = "t.test")
```
## 2.2 violinplot of domain size(with boxplot)
```{r fig.height=6, fig.width=8}
library(ggpubr)
my_comparisons <- list(c("U2OS", "Clone110"), c("U2OS", "FUSClone110"))
p<- ggviolin(all_sample_segway_v2, x = "sample",
y = "domain_size",
facet.by = "domain",
short.panel.labs = TRUE,
legend.title ="",
x.text.angle = 45,
xlab ="Replication Domain",
ylab = "Domain Size (bp)",
color = "sample",
palette = "aaas",
add = "boxplot"
# add = "median_iqr"
)+
yscale("log10", .format = TRUE)+
stat_compare_means(comparisons = my_comparisons, aes(label = paste0("p = ", ..p.format..)),
method = "t.test", label.y = c(7.7, 8))
p
```
# 3.Summary of Replication timing domain
## 3.1 table of RT domain count
```{r}
RT_sum <- count(all_sample_segway_v2, vars = c("sample","domain"))
RT_sum
# get median value of each domain in each sample
U2OS_E <- subset(U2OS_segway_v2, grepl('E', domain))
Clone110_E <- subset(Clone110_segway_v2, grepl('E', domain))
FUSClone110_E <- subset(FUSClone110_segway_v2, grepl('E', domain))
summary(U2OS_E$domain_size)
summary(Clone110_E$domain_size)
summary(FUSClone110_E$domain_size)
sum(U2OS_E$domain_size)
# cat(paste("Median:", median(FUSClone110_E$domain_size)))
```
## 3.2 barplot of RT domain count
```{r fig.height=5, fig.width=4}
ggbarplot(RT_sum, x="sample",
y= "freq",
ylab = "Domain Count",
xlab = "",
legend.title ="Domain",
color = "domain",
fill = "domain",
palette = "aaas",
label = TRUE,
lab.pos = "in",
width = 0.6,
#add = "median",
lab.col = "white"
#position = position_dodge(0.9)
#order = c()
#orientation = "horiz"
)+
scale_y_continuous(expand = c(0, 0))
```
## 3.3 barplot of RT domain coverage
```{r fig.height=5, fig.width=4}
library(dplyr)
Domain_sum <- all_sample_segway_v2 %>%
tidyr::drop_na()%>%
dplyr::group_by(sample, domain)%>%
dplyr::summarise(domain_size_sum= sum(domain_size))
Domain_sum<- Domain_sum%>%
dplyr::mutate(Percentage=round(100*domain_size_sum/sum(domain_size_sum), 2))
Domain_sum
ggbarplot(Domain_sum, x="sample",
y= "Percentage",
ylab = "Genome Coverage (%)",
xlab = "",
legend.title ="Domain",
color = "domain",
fill = "domain",
palette = "aaas",
label = TRUE,
lab.pos = "in",
width = 0.6,
lab.col = "white"
)+
scale_y_continuous(expand = c(0, 0))
```
```{r}
sessionInfo()
```