ubuntu linux虚拟机搭建+PopLDdecay

1.可以直接在Microsoft store中下载ubuntu

，如果没有使用过打开是这样的

Installing, this may take a few minutes...
WslRegisterDistribution failed with error: 0x8007019e
Error: 0x8007019e ??????? Linux ? Windows ????

Press any key to continue...

2.控制面板里打开这三个

参照官网进行安装

下载并安装

https://wslstorestorage.blob.core.windows.net/wslblob/wsl_update_x64.msi

terminal运行

wsl --set-default-version 2

关闭终端

打开ubuntu

设置账号密码 /密码输入的时候是不显示的

进入linux

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miniconda 搭建虚拟环境

http://t.csdnimg.cn/hf9fg

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4.PopLDdecay安装

sudo apt update

# 安装 build-essential 包（包含 gcc、g++ 和 make）
sudo apt install build-essential

sudo apt install zlib1g-dev

#安装PopLDdecay
git clone https://github.com/BGI-shenzhen/PopLDdecay.git
cd PopLDdecay
chmod 755 configure
./configure
make
mv PopLDdecay ./bin/
 
# 打开 .bashrc 文件
nano ~/.bashrc

# 在文件末尾添加以下行（使用您的实际路径）
export PATH="/mnt/f/linux_zky/PopLDdecay-master/bin:$PATH"

# 保存并退出 nano（按 Ctrl+X，然后 Y，最后 Enter）

# 使更改生效
source ~/.bashrc

# 验证 PATH 更新
echo $PATH

环境变量配置成功

5.使用PopLDdecay计算

PopLDdecay -InVCF /mnt/e/pyProjects/zc/2024年8月23日/ZC-wanglin分析/data/clean.vcf -OutStat LDdecay

当前路径下生成结果文件 LDdecay.stat.gz

6.下载Rstudio

       下载R

安装R 

安装Rstudio

参数没搞懂怎么设置

反正能跑

先计算出ld.stat
PopLDdecay -InVCF clean.vcf -MaxDist 5000 -OutStat ld.stat

可以用自带的工具直接出图

../PopLDdecay-master/bin/Plot_OnePop.pl -inFile /mnt/f/linux_zky/zc_LD/ld.stat.gz --output re1 -bin1 10 -bin2 100

也可以用R自己做

# 清除工作环境中的变量
rm(list = ls())

# 设置工作目录
setwd("E:/pyProjects/zc/2024年8月23日")

# 加载必要的库
library(ggplot2)
library(dplyr)

# 读取数据并设置正确的列名
ld_data <- read.table("F:/linux_zky/zc_LD/ld.stat", header = TRUE, sep = "\t") %>%
  setNames(c("Distance", "r2", "NA1", "r2_mean", "NA2", "Count"))

# 参数设置
bin1 <- 10
bin2 <- 100
break_point <- 1000

# 数据处理函数
process_data <- function(data, bin_size, break_point) {
  data %>%
    mutate(bin = ifelse(Distance < break_point,
                        floor((Distance - 0.1) / bin_size) * bin_size,
                        floor((Distance - 0.1) / bin_size) * bin_size + break_point)) %>%
    group_by(bin) %>%
    summarise(mean_r2 = mean(r2, na.rm = TRUE),
              count = sum(Count)) %>%
    arrange(bin)
}

# 处理数据
small_bins <- process_data(filter(ld_data, Distance < break_point), bin1, break_point)
large_bins <- process_data(filter(ld_data, Distance >= break_point), bin2, break_point)

# 合并数据
combined_data <- bind_rows(small_bins, large_bins) %>% arrange(bin)
# 创建LD衰减图（热图风格和平滑处理，减少 x 轴密度）
ld_plot <- ggplot(combined_data, aes(x = bin, y = mean_r2)) +
  geom_point(aes(color = bin), alpha = 0.5, size = 1) +
  geom_smooth(method = "loess", color = "black", se = FALSE, size = 1) +
  scale_color_gradient(low = "blue", high = "red") +
  scale_x_continuous(
    breaks = seq(0, max(combined_data$bin), by = 200000),  # 增加间隔到 200,000
    labels = function(x) paste0(x/1000000, "Mb"),
    expand = c(0.01, 0)  # 稍微扩展 x 轴以避免点被切off
  ) +
  scale_y_continuous(limits = c(0, 1)) +
  theme_minimal() +
  theme(
    legend.position = "right",
    plot.title = element_text(face = "bold", size = 14, hjust = 0.5),
    axis.title = element_text(size = 12),
    axis.text = element_text(size = 10),
    axis.text.x = element_text(angle = 45, hjust = 1),  # 旋转 x 轴标签以避免重叠
    plot.margin = margin(5.5, 14, 5.5, 14)
  ) +
  labs(
    title = "LD Decay Plot (Smoothed)",
    x = "Distance (Kb)",
    y = expression(r^2),
    color = "Distance (Mb)"
  )


# 保存图形
ggsave("LD_decay_plot_smoothed_heatmap_reduced_density.png", ld_plot, width = 12, height = 6, dpi = 300)