Description Usage Arguments Details Value Note Author(s) See Also Examples
The function manPlotFast
creates a Manhattan plot.
The function manPlotPrepare
extracts necessary information
from a vector of p-values sufficient for creating a Manhattan plot.
It optimized to work quickly even for tens of millions of p-values.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | manPlotPrepare(
pvalues,
chr,
pos,
ismlog10 = FALSE,
chrmargins = 5e6)
manPlotFast(
man,
ylim = NULL,
colorSet = c('steelblue4',"#2C82D1","#4CB2D1"),
yaxmax = NULL,
lwd = 3,
axistep = 2,
cex = 1)
|
pvalues |
Vector of p-values.
As is (if |
chr, pos |
Vectors indicating the chromosomes and genomic positions (in basepairs)
for each p-value in |
ismlog10 |
Specifies whether the provides p-values ( |
chrmargins |
The plot margins at the ends of chromosomes (in basepairs). |
man |
Object returned by |
ylim |
Numeric vectors of length 2, giving the y coordinate range. Exactly as in Plotting Parameters. |
colorSet |
Colors of points, rotating over chromosomes. |
yaxmax |
Maximum reach of the y axis. |
lwd |
The line width. |
axistep |
Distance between axis label ticks for y axis. |
cex |
The size of Manhattan plot points. As in Graphics Parameters. |
The function manPlotFast
creates Manhattan plot.
It requires the use of the function manPlotPrepare
which extracts the necessary information
from a vector of p-values sufficient for creating Manhattan plot.
The resulting object is many times smaller than the vector of p-values.
This function manPlotPrepare
returns an object with
information for creating Manhattan plot.
The plot has no title. To add a title use title
.
Andrey A Shabalin andrey.shabalin@gmail.com
See vignettes: browseVignettes("ramwas")
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | # Simulate data (9 chromosomes, million tests each)
chr = rep(paste0('chr',1:9), each = 1e6)
pos = rep(1:1e6, 9)
pv = runif(9e6)^1.1
# Extract the Manhattan plot info
man = manPlotPrepare(pv, chr, pos, chrmargins = 1000)
# Create Manhattan plot
manPlotFast(man)
title("Manhattan plot")
# Size of p-values before extraction of Manhattan plot info
object.size(list(pv, chr, pos))
# Size of the Manhattan plot info object
object.size(man)
|
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