Hi all,

I have a tab delimited file with the following columns:

```
CHR SNP bp Fst
```

where Fst is the fixation index. Does anyone know how to make a Manhattan plot of these Fst values in R? Many thanks!

R: Manhattan Plot Of Fst Values Instead Of -Log(P)

3

Entering edit mode

12.2 years ago

Abdel
▴
410

Hi all,

I have a tab delimited file with the following columns:

```
CHR SNP bp Fst
```

where Fst is the fixation index. Does anyone know how to make a Manhattan plot of these Fst values in R? Many thanks!

6

Entering edit mode

12.2 years ago

John
★
1.5k

I found the following blog useful, you need tweak the codes to fit F-value not -log10(p) value - http://gettinggeneticsdone.blogspot.com/2011/04/annotated-manhattan-plots-and-qq-plots.html

Edits:

If you would like to use lattice or ggplot, we can create similar plot:

```
# just an example
Fst <- rnorm(10000, 10, 5)
chr <- c(rep(1, 2500), rep(2, 2500), rep(3, 2500), rep(4, 2500))
BP <- c(1:2500, 1:2500, 1:2500, 1:2500)
mydf <- data.frame (Fst, chr, BP)
require(ggplot2)
qplot(BP, Fst, facets = . ~ chr, col = factor(chr), data = mydf)
```

I like bw theme better

```
qplot(BP, Fst, facets = . ~ chr, col = factor(chr), data = mydf) + theme_bw()
```

You need to reshape plot area or change arrangement of graph to make all facets in single line as Manhattan plot. The graph is pretty close but not exactly as in above blog code.

3

Entering edit mode

12.2 years ago

Zev.Kronenberg
12k

I have done the exact plot you want for FST.

here is where [R] becomes awesome:

```
dat<-read.csv("your.data.txt", header=FALSE, sep="\t")
plot(dat$FST, col=as.factor(dat$CHR))
```

If you need the true coordinates ie BP I will send you a script I wrote to take that into account. Otherwise the code above will suffice.

Pretty much R gives the X values a number `1:length(dat$FST)`

and then colors the points by the `dat$CHR`

0

Entering edit mode

Hi all,

I need to do the same plot as described above but I am facing the same problem.

```
plot(dat$FST, col=as.factor(dat$CHR))
Error in plot.window(...) : need finite 'xlim' values
In addition: Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf
3: In min(x) : no non-missing arguments to min; returning Inf
4: In max(x) : no non-missing arguments to max; returning -Inf
```

what I have to do? what do you mean by `head(dat)`

?

Thanks in advance

0

Entering edit mode

9.5 years ago

CB
▴
10

I want to create a Manhattan plot to plot Fst values of each SNP. I used John's first code to plot Fst values for 3 different chromosomes and it worked well. But the size of chromosomes are fixed, and I want to set the maximum size for each chromosome. Is it possible? The code that I used was:

```
Fst <- rnorm(48167,0.13, 0.2)
chr <- c(rep(1, 14552), rep(2, 33582), rep(10, 33))
BP <- c(1:14552, 1:33582, 1:33)
data <- data.frame (Fst, chr, BP) qplot(BP, Fst, facets = . ~ chr, col = factor(chr), data = data)
```

I tried to use the package qqman to plot Fst values instead of P values and did not work.

Or I need to use the perl script that Zev.Kronenberg mentioned? Convert chrmosomes positions into genomic coordiantes?

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You just have to replace bp by BP and Fst by P and it should work.