在GWAS/曼哈顿图中无法正确重复颜色--颜色不一致

Question

我使用ggplot2将GWAS汇总统计数据绘制为曼哈顿图。事情就像预期的一样，但是颜色没有正确地重复。无论我是重复2种颜色还是4种颜色，在早期都会有一次重复，导致两条染色体相邻成相同的颜色。即使我手动定义了所有的染色体颜色，我仍然在相邻的两个染色体之间有重复。我不确定为什么或者我做错了什么？

如有任何帮助，我们不胜感激！我的代码如下：

# read in data
data <- read.table(args[1], header = TRUE)
pval = args[2]
data = as.data.frame(data)
data[pval] <- lapply(data[pval], as.numeric)


# load libraries
library(ggplot2)
library(dplyr)
data$BPcum <- NA
s <- 0
nbp <- c()
for (i in unique(data$CHR)){
  nbp[i] <- max(data[data$CHR == i,]$BP)
  data[data$CHR == i,"BPcum"] <- data[data$CHR == i,"BP"] + s
  s <- s + nbp[i]
}

axisdf = data %>% group_by(CHR) %>% summarize(center=( max(BPcum) + min(BPcum) ) / 2 )


# -log10(pval) and bonferonni cut off
data$logp <- -log10(data[pval])
bofferroni<- -log10(0.05/dim(data)[1])


# filter data so it can graph a little more easily
data<-data[!(data[pval]==0),]
data <- filter(data, data[pval] < 1e-1)
data$logp = unlist(data$logp)

# plot
plot <- ggplot(data, aes(x=BPcum, y=logp)) +

  # add bofferroni cut off
  geom_hline(yintercept=bofferroni, color = "red", size=.65) +

  # show all points
  geom_point( aes(color=as.factor(CHR)), alpha=0.4, size=1.3) +
  scale_color_manual(values = rep(c("#D2A18C", "#785C50"), 12)) +

  # custom X axis:
  scale_x_continuous( label = axisdf$CHR, breaks= axisdf$center ) +

  # remove space between plot area and x axis
  scale_y_continuous(expand = c(0, 0) ) +

  # add title and lables
  ggtitle(paste(args[2],"Manhattan Plot")) +
  xlab("BP") + ylab("-log10(PVALUE)") +

  # custom the theme:
  theme_bw() +
  theme(
    legend.position="none",
    panel.border = element_blank(),
    panel.grid.major.x = element_blank(),
    panel.grid.minor.x = element_blank()
  )


pdf(paste("gwasplot", args[2], args[1], ".pdf", sep="_"), height=6, width=12)
plot
dev.off()

Answer 1

好的，我从一个修复了这个问题的同事那里得到了帮助，我们需要重新排序CHR的水平，因为它们的顺序是“1，10，11，12…2，21，22“等，而不是”1，2，3，4…“。为此，我添加了下面这一行

# reorder factor levels for plot 
data$CHR = factor(data$CHR, levels = c("1",  "2",  "3",  "4",  "5", "6", "7",  "8",  "9", "10",
                                       "11", "12", "13", "14", "15", "16", "17", "18", "19", "20",
                                       "21", "22", "23", "24", "X"))

我还改变了这个

geom_point( aes(color=as.factor(CHR)), alpha=0.4, size=1.3) +

至

geom_point( aes(color=CHR), alpha=0.4, size=1.3) +

希望这对其他人有帮助！