The plot below is what I want to plot: 
![enter image description here][1]

Basically, the plot contains the log(Pi1/Pi2) values for specific positions on each chromosome. (It looks like a Manhattan plot but with negative values)

I have the following data frame 

    Chromosome  Position  Log_Pi
    
    1              102331    -0.552
    2              220231    2.32
    5              233433   -2.200
    .
    .
    .
    7             522631   -1.023
    7             322512    1.2231
    10            233356      -0.223
    12            5666932     0.2235


I have tried: 

    ggplot(data = Pi_PLOT, aes(x = Chromosome, y = log_pi)) + geom_point(data = Pi_PLOT, aes(x = Position, y = log_pi, fill = Chromosome)) + labs(x = "Chromosome", y = "log_pi")

  [1]: /media/images/b3c1418c-55f8-4613-9257-e700c256

I figured out by using the [CMplot package](https://cran.r-project.org/package=CMplot) in R.

Thanks