Miami plot
Usage
miamiplot(
x,
chr = "CHR",
bp = "BP",
p = "P",
pr = "PR",
snp = "SNP",
col = c("midnightblue", "chartreuse4"),
col2 = c("royalblue1", "seagreen1"),
ymax = NULL,
highlight = NULL,
highlight.add = NULL,
pch = 19,
cex = 0.75,
cex.lab = 1,
xlab = "Chromosome",
ylab = "-log10(P) [y>0]; log10(P) [y<0]",
lcols = c("red", "black"),
lwds = c(5, 2),
ltys = c(1, 2),
main = "",
...
)Arguments
- x
Input data.
- chr
Chromsome.
- bp
Position.
- p
P value.
- pr
P value of the other GWAS.
- snp
Marker.
- col
Colors.
- col2
Colors.
- ymax
Max y.
- highlight
Highlight flag.
- highlight.add
Highlight meta-data.
- pch
Symbol.
- cex
cex.
- cex.lab
cex for labels.
- xlab
Label for x-axis.
- ylab
Label for y-axis.
- lcols
Colors.
- lwds
lwd.
- ltys
lty.
- main
Main title.
- ...
Additional options.
Details
The function allows for contrast of genomewide P values from two GWASs. It is conceptually simpler than at the first sight since it involves only one set of chromosomal positions.
Examples
if (FALSE) { # \dontrun{
mhtdata <- within(mhtdata,{pr=p})
miamiplot(mhtdata,chr="chr",bp="pos",p="p",pr="pr",snp="rsn")
} # }