ggplot Manhattan plotΒΆ

[1]:
library(ggplot2)
df = read.table("ggplot_input.tsv",header=TRUE)
df[sample(dim(df)[1],5),]
mid_pointlogFDRgroup
7285306044 2.79290446APC
2965306035 0.16209606GFP
6205264931 0.01026105APC
4415245952 300.00000000APC
8295319376 1.24517023APC
[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
../_images/jupyter_notebooks_ggplot_manhattan_2_2.png
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