manhattan {ramwas} | R Documentation |
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.
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")
.
# 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)