manhattan plot

[Hermann Norpois]

Hello,

I dont find a proper and simple way to produce a manhattan plot (y-axis: -log pval, x-axis: chr and bp).

I think of a syntax like this:
ggplot (df)+ geom_point (aes (x=bp, y= -log p))
...but I dont have an idea how to deal with the chromosomes (chr).

Thanks
Hermann

> df
  snp chr bp    p
1 rs1   1 12 0.02
2 rs2   1 14 0.40
3 rs4   2 16 0.05
4 rs6   2 20 0.08
5 rs8   3 14 0.07
> dput(df)
structure(list(snp = structure(1:5, .Label = c("rs1", "rs2",
"rs4", "rs6", "rs8"), class = "factor"), chr = c(1, 1, 2, 2,
3), bp = c(12, 14, 16, 20, 14), p = c(0.02, 0.4, 0.05, 0.08,
0.07)), .Names = c("snp", "chr", "bp", "p"), row.names = c(NA,
-5L), class = "data.frame")

[William Beasley]

I like the facets for this.  But if you didn't want facets (and instead wanted one big frame), Winston's new book has a very similar example in Section 3.10 (Fig 3-30).  MLB batters are sorted by league (ie chromosome), and then by the batting average (ie, bp).

[Winston Chang]

FWIW, here's the code and the image that William is referring to:

library(gcookbook) # For the data set

library(ggplot2)

tophit <- tophitters2001[1:25, ] # Take the top 25 from the tophitters data set

# Get the names, sorted first by lg, then by avg

nameorder <- tophit$name[order(tophit$lg, tophit$avg)]

# Turn name into a factor, with levels in the order of nameorder

tophit$name <- factor(tophit$name, levels=nameorder)

ggplot(tophit, aes(x=avg, y=name)) +

    geom_segment(aes(yend=name), xend=0, colour="grey50") +

    geom_point(size=3, aes(colour=lg)) +

    scale_colour_brewer(palette="Set1", limits=c("NL","AL")) +

    theme_bw() +

    theme(panel.grid.major.y = element_blank(),   # No horizontal grid lines

          legend.position=c(1, 0.55),             # Put legend inside plot area

          legend.justification=c(1, 0.5))

-Winston

On Wed, Mar 13, 2013 at 5:40 PM, William Beasley <wibe...@hotmail.com> wrote:

I like the facets for this.  But if you didn't want facets (and instead wanted one big frame), Winston's new book has a very similar example in Section 3.10 (Fig 3-30).  MLB batters are sorted by league (ie chromosome), and then by the batting average (ie, bp).

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[Hermann Norpois]

Thanks.
This was very helpful.
But I still have question.

I modified your example for my purpose but there is something missing and I dont know how to do. Prinicpally the "picture" is phantastic. But on the x axis I need the numbers of the chromosomes (instead of bp). The dots are plotted in dependence of bp (so geom_point (aes (x=bp, y=mlp)...  This is correct but I dont want the bps to be listed at the x-axis. But I want to see the numbers of the chromosome only.

Thanks
Hermann

ggplot(df) +
    geom_point(aes(x=bp, y= mlp), size=3, colour = ifelse (chr %% 2 ==1, "black", "grey")) +
    ylab ("-log pval")+

    theme_bw() +
    theme(panel.grid.major.y = element_blank(),   # No horizontal grid lines

          panel.grid.major.x = element_blank(),

          legend.position=c(1, 0.55),             # Put legend inside plot area
          legend.justification=c(1, 0.5))

> dput (df)
structure(list(snp = structure(c(1L, 4L, 5L, 6L, 7L, 2L, 3L), .Label = c("snp1",
"snp10", "snp11", "snp2", "snp3", "snp5", "snp6"), class = "factor"),
    chr = structure(c(1L, 1L, 1L, 2L, 2L, 3L, 3L), .Label = c("1",
    "2", "3"), class = "factor"), bp = structure(c(2L, 3L, 4L,
    5L, 7L, 1L, 6L), .Label = c("10", "12", "14", "15", "2",
    "20", "6"), class = "factor"), p = c(3, 4, 5, 2, 3, 2, 1),
    mlp = c(3.91202300542815, 3.50655789731998, 3.2188758248682,
    4.60517018598809, 3.91202300542815, 4.60517018598809, 5.52146091786225
    )), .Names = c("snp", "chr", "bp", "p", "mlp"), row.names = c(NA,
-7L), class = "data.frame")

2013/3/14 Winston Chang <winsto...@gmail.com>

[William Beasley]

I can think of several fancier ways to do this (including defining a formatter function), but here's a simple manual way that indicates the chromosome on the first bp within each batch.

Define these before the declaration of the graphing code:

bpBreaks <- as.character(c(10, 12, 14, 15, 2, 20, 6))

bpLabels <- c("1", "", "", "2", "", "3", "")  

Add this to the graphing code:

scale_x_discrete(breaks=bpBreaks, labels=bpLabels) + xlab("Chromosome") +