Add a CpG density track by using bsseq to find all CpG sites in the genome and adding up CpG sites at each distance from the repeat start and end, plot as tile – light blue = high CpG content, dark blue = low CpG content

Removed 18 row(s) containing missing values (geom_path).Removed 18 rows containing missing values (geom_point).

---
title: "Composite Element Methylation TELOclusters"
author: "Ariel"
date: "`r format(Sys.time(), '%B %d, %Y')`"
output:
  pdf_document: default
  html_document:
    df_print: paged
  html_notebook: default
mainfont: DejaVu Sans
titlefont: DejaVu Sans
---

```{r include=FALSE}
knitr::opts_chunk$set(echo = FALSE, warning=FALSE,  message=FALSE)

# these are my personal utils -- find them in the utils dir of the T2T-Epigenetics git repo
source("~/T2T-Epigenetics/utils/ilee_plot_utils.R")
source("~/T2T-Epigenetics/utils/methylation_R_utils.R")
library(tidyverse)
library(cowplot)
library(zoo)
library(bsseq)
# BSgenome package for T2T genome -- find on globus and install
library(BSgenome.t2t.v1.0.release)

figs="/kyber/Data/Nanopore/Analysis/gmoney/CHM13/v1.0_final_assembly/figures"
dat="/kyber/Data/Nanopore/Analysis/gmoney/CHM13/v1.0_final_assembly"
```

```{r loadData, include=F}
dat="/kyber/Data/Nanopore/Analysis/gmoney/CHM13/v1.0_final_assembly"
chm13_meth <- read_tsv(paste0(dat, "/methylation_calls/methylation_frequency_50kb_split.tsv")) %>%
  GRanges()

regs <- read_tsv(paste0(dat, "/TE/TeloComposites/TELO-composite-unitA_RM-polish_APR2121_SHoyt.txt"), col_names = T) %>%
  mutate(len=end-start) %>%
  filter(len>0) %>%
  filter(len<3000) %>%
  mutate(ID=n())

```

```{r 5kb, echo=F}

# size of flanking region
flankn <- 20000
# size of repeat relative to flanking region
bodylen <- 1/5

# add flanks
l1_regions <- regs %>%
  mutate(start = start - flankn, end = end + flankn) %>%
  GRanges()

# add methylation data
ovl <- findOverlaps(chm13_meth, l1_regions)
genes.ovl <- as.data.frame(regs)[subjectHits(ovl),] %>%
  dplyr::mutate(genewidth = end - start) %>%
  dplyr::rename(gene_start = start, gene_end = end) 

# calculate distance from start and end, depending on strand 
chm13.ovl <- as.data.frame(chm13_meth[queryHits(ovl),]) %>%
  bind_cols(genes.ovl) %>%
  dplyr::rename(seqnames = 1) %>%
  mutate(dist = ifelse(Orientation=="pos", start - gene_start, gene_end-start)) %>%
  mutate(dist = ifelse(dist < 0, dist/flankn,
      ifelse(dist < genewidth,
        bodylen * dist / genewidth,
        bodylen + (dist - genewidth)/flankn)), 
    dist = round(dist,2)
    )

# bin data to make plot pretty
n_windows=1000
chm13.ovl$cut = cut(chm13.ovl$dist, breaks=n_windows)

chm13.ovl.labs <- chm13.ovl %>%
  group_by(cut,`49bp_yes/no`) %>%
  summarise(med = median(methylated_frequency), top = quantile(methylated_frequency, 0.75), bot = quantile(methylated_frequency, 0.25), n_genes = length(methylated_frequency)) %>%
  mutate(x_tmp = str_sub(cut, 2, -2)) %>% 
  separate(x_tmp, c("min", "max"), sep = ",") %>% 
  mutate_at(c("min", "max"), as.double) %>%
  ungroup() %>%
  group_by(`49bp_yes/no`) %>%
  arrange(min) %>%
  mutate(med_smooth = rollmean(med, 10, NA))

# plot -- include annotation for number of repeats in each group
p <- ggplot(chm13.ovl.labs,aes( x = min, y = med_smooth, color=`49bp_yes/no`, fill=`49bp_yes/no`), alpha=.5)+
  geom_ribbon(aes(ymin=bot, ymax=top), alpha=0.2, size=0)+
  geom_line(aes(y=med_smooth), alpha=.5, size=1) +
  geom_vline(xintercept = 0) +
  geom_vline(xintercept = bodylen)+
  geom_point(alpha=.5)+
  labs( x = "Genomic Position", y = "Aggregated Methylation Frequency") +
  theme_classic()+scale_x_continuous(breaks= c(-1,0,bodylen,bodylen + 1), labels = c(paste0("-",flankn/1e3,"kb"),"Start","End",paste0("+",flankn/1e3,"kb")))+
geom_text(data = chm13.ovl %>% 
              group_by(`49bp_yes/no`) %>%
              select(`49bp_yes/no`,gene_start) %>%
              distinct() %>%
              summarise(n_genes=n()) %>%
              distinct() %>%
              mutate(height=case_when(`49bp_yes/no` == "yes" ~ 0, 
                          `49bp_yes/no` == "no" ~ .1, 
                          TRUE ~ .02)),
            aes(x=1,
                y=.85+height,
                label=paste("n =",comma(n_genes))
                ), hjust=1)+
theme(legend.position = "top")


p


ggsave(
  paste0(figs, "/evol_meth/TE/","CHM13_subTELO_metaplot.pdf"),
  plot = p,
  scale = 1,
  width = 12,
  height = 5,
)
```



Add a CpG density track by using bsseq to find all CpG sites in the genome and adding up CpG sites at each distance from the repeat start and end, plot as tile -- light blue = high CpG content, dark blue = low CpG content 

```{r}

# count CG sites from bsseq package -- takes a hot sec, save as rbs file for future use
t2t.cpg.loci <- findLoci(pattern = "CG",
                         subject = BSgenome.t2t.v1.0.release::BSgenome.t2t.v1.0.release, 
                         strand = "+")
# you should count ~32M CpGs
length(t2t.cpg.loci)

# now find overlaps between CpG sites and repeats
l1_regions <- regs %>%
  mutate(start = start - flankn, end = end + flankn) %>%
  GRanges()

ovl <- findOverlaps(t2t.cpg.loci, l1_regions)
genes.ovl <- as.data.frame(regs)[subjectHits(ovl),] %>%
  dplyr::mutate(genewidth = end - start) %>%
  dplyr::rename(gene_start = start, gene_end = end) 

chm13.ovl <- as.data.frame(t2t.cpg.loci[queryHits(ovl),]) %>%
  bind_cols(genes.ovl) %>%
  dplyr::rename(seqnames = 1) %>%
  dplyr::mutate(dist = ifelse(Orientation == "pos",start - gene_start, gene_end - start),
    dist = ifelse(dist < 0, dist/flankn,
      ifelse(dist < genewidth,
        bodylen * dist / genewidth,
        bodylen + (dist - genewidth)/flankn)), 
    dist = round(dist,2)
    )

# plot CpG density as heatmap -- the actual number doesnt mean anything, its just for visualization
chm13.ovl.labs <- chm13.ovl %>%
  group_by(ID) %>%
  mutate(total=n()) %>%
  ungroup() %>%
  group_by(dist) %>%
  summarise(med = sum(width), cg=med/total) %>%
  distinct()
  
q <- ggplot(chm13.ovl.labs, aes(x=dist,y=1, fill=cg))+geom_tile()+scale_x_continuous(breaks= c(-1,0,bodylen,bodylen + 1), labels = c(paste0("-",flankn/1e3,"kb"),"Start","End",paste0("+",flankn/1e3,"kb")))+theme_void()+theme(legend.position = "none")

# use cowplot to combine plots on the same X-axis
plot_grid(p,q, ncol=1, align = "v",rel_heights = c(3,.5))
```







