ks_plot.md

setwd("E:/Li/flower_color/wgd/Ks_plots-master/")

r_files <- list.files(pattern = "\.R$")

逐个加载这些文件

for (file in r_files) { source(file) }

x <- read.table("Pflo.ksNG86",header = T)

ks_NG86 <- x$ks_NG86

summary(ks_NG86) # 查看数据摘要

ploidy_result <- ploidy.test(ks_NG86)

自动模型选择

bic_results <- bic.test.wgd( x = ks_NG86, startK = 2, maxK = 5, model = 1, nstarts = 100, outPrefix = "pf_raw_bic" )

手动优化（示例）

K4 <- mixEM(ks_NG86, k=4, model=4, nstarts=100) K3 <- mixEM(ks_NG86, k=3, model=4, nstarts=100) K2 <- mixEM(ks_NG86, k=2, model=4, nstarts=100) print(K4) print(K3) print(K2)

绘图

打开 PDF 设备

pdf("K4plotComponents.pdf", width = 8, height = 6)

绘制图形

plotComponents( x = ks_NG86, lambda = K4$lambda, params = K4$parameters, model = 4 )

关闭 PDF 设备

dev.off()

打开 PDF 设备

pdf("K3plotComponents.pdf", width = 8, height = 6)

绘制图形

plotComponents( x = ks_NG86, lambda = K3$lambda, params = K3$parameters, model = 4 )

关闭 PDF 设备

dev.off()

关闭 PDF 设备

dev.off()

打开 PDF 设备

pdf("K2plotComponents.pdf", width = 8, height = 6)

绘制图形

plotComponents( x = ks_NG86, lambda = K2$lambda, params = K2$parameters, model = 1 )

关闭 PDF 设备

dev.off()

library(ggplot2)

p2 <- ggplot(x, aes(x = ks_median)) + geom_density(color = "darkblue", fill = "lightblue", alpha = 0.5)

pdf("basedist.pdf", width = 8, height = 6) p2 dev.off()