LDproxy.Rmd

---
title: "LDproxy"
author: "Keren Xu"
date: "7/18/2021"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(ggpubr)
theme_set(theme_light())
```

```{r}
library(haploR)
library(tidyverse)
library(data.table)
library(ggplot2)

rs78396808 <- fread("proxy34387_rs78396808.txt")
rs6421315 <- fread("proxy75653_rs6421315.txt")

df_rs78396808 <- rs78396808 %>% select(RS_Number, R2) %>% rename("R2_rs78396808" = "R2")
df_rs6421315 <- rs6421315 %>% select(RS_Number, R2) %>% rename("R2_rs6421315" = "R2")
df_total <- df_rs78396808 %>% filter(RS_Number != ".") %>% inner_join(df_rs6421315, by = "RS_Number") 

rs78396808 %>% filter(RS_Number == ".")%>% filter(!is.na(Correlated_Alleles))
rs6421315 %>% filter(RS_Number == ".")%>% filter(!is.na(Correlated_Alleles))
```

```{r, fig.width= 6, fig.height = 5}
df_total %>% ggplot(aes(x = R2_rs78396808, y = R2_rs6421315)) + 
  geom_point(
        color="black",
        fill="grey",
        shape=21,
        alpha=0.5,
        size=2
        ) + 
  labs(
    x = bquote('AMR'~R^2~'with rs78396808'), 
    y = bquote('EUR'~R^2~'with rs6421315')) + 
  scale_x_continuous(limits = c(0, 1)) + 
  scale_y_continuous(limits = c(0,1))
```