ggplot Manhattan plotΒΆ
[1]:
library(ggplot2)
df = read.table("ggplot_input.tsv",header=TRUE)
df[sample(dim(df)[1],5),]
mid_point | logFDR | group | |
---|---|---|---|
728 | 5306044 | 2.79290446 | APC |
296 | 5306035 | 0.16209606 | GFP |
620 | 5264931 | 0.01026105 | APC |
441 | 5245952 | 300.00000000 | APC |
829 | 5319376 | 1.24517023 | APC |
[2]:
ggplot(df,aes(x=mid_point,y=logFDR))+
geom_point( aes(color=group), alpha=0.6, size=1.5)+
scale_x_continuous(name="chr11",breaks=seq(5239000,5329000,5000))+
scale_y_continuous(name="-log10(FDR)")+
theme_bw() +
theme(
panel.border = element_blank(),
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
axis.text.x = element_text(angle = 30, hjust = 1)
)
ggsave("figure.png",dpi=300)
Saving 6.67 x 6.67 in image
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