How to plot allele frequency

Question

[mostafarafiepour]

Hi all,

I have a table that you will see below:

         CHROM_POS   A_Freq      M.F Annotation    N_Chr  POP
1   CM009840.1_932 1.000000 0.000000   nongenic 20.00000 KHUZ
2  CM009840.1_1096 0.666667 0.333333   nongenic 13.33334 KHUZ
3  CM009840.1_1107 0.277778 0.277778   nongenic  5.55556 KHUZ
4  CM009840.1_1177 0.500000 0.500000   nongenic 10.00000 KHUZ
5  CM009840.1_1276 0.555556 0.444444   nongenic 11.11112 KHUZ
6  CM009840.1_1295 0.555556 0.444444   nongenic 11.11112 KHUZ
7  CM009840.1_1518 0.937500 0.062500   nongenic 18.75000 KHUZ
8  CM009840.1_1527 0.000000 0.000000   nongenic  0.00000 KHUZ
9  CM009840.1_1533 0.937500 0.062500   nongenic 18.75000 KHUZ
10 CM009840.1_1630 0.062500 0.062500   nongenic  1.25000 KHUZ

SO, I want to draw a plot like the following plot:

What is the best idea?

Answer 1

[zx8754]

Here is a start:

library(dplyr)
library(ggplot2)

# example data
set.seed(1); myData <- data.frame(
  A_Freq = runif(1000),
  Annotation = sample(LETTERS[1:3], 1000, replace = TRUE))

# prepare data, use "cut" make "A_Freq" groups
plotDat <- myData %>% 
  mutate(AlleleFrequency = cut(A_Freq, seq(0, 1, 0.25))) %>% 
  group_by(AlleleFrequency, Annotation) %>% 
  summarise(FractionOfSNPs = n()/nrow(myData) * 100)

# then plot
ggplot(plotDat,
       aes(AlleleFrequency, FractionOfSNPs, group = Annotation, col = Annotation)) +
  geom_line() +
  scale_y_continuous(limits = c(0, 100))