输出coords 文件
展示一条染色体
library(ggplot2)
file <- "C:\\Users\\Admin\\Desktop\\"
nucmer <- read.delim(paste0(file, "nucmer.coords"),
header = F,
sep = "\t",
stringsAsFactors = FALSE)
colnames(nucmer) <- c("ref_start", "ref_end", "qry_start", "qry_end",
"ref_len", "qry_len", "identiy", "ref_tag","qry_tag")
chr1_nuc <- subset(nucmer, ref_tag == 'chr1' & qry_tag == 'chr1')
ggplot(data = chr1_nuc) +
geom_segment(aes(x = ref_start/100000, y = qry_start/100000,
xend = ref_end/100000,
yend = qry_end/100000), size = 1)+
xlab(label = "ref genome") +
ylab(label = "qry genome") +
theme_bw()
展示所有染色体
ggplot(data = nucmer) + facet_grid(qry_tag~ref_tag, as.table = FALSE,
switch = "both", scales = "free",
space = "free") +
geom_segment(aes(x = ref_start/10000, y = qry_start/10000,
xend = ref_end/10000,
yend = qry_end/10000), size = 1) +
scale_colour_gradient(low = "black",
high = "red") +
theme_bw() +
xlab(label = "ref genome") +
ylab(label = "qry genome")
