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#####################################################################
#
# plotRsq.R
#
# copyright (c) 2008-3, Ahmid A Khalili
#
# last modified Jul, 2008
# first written Mar, 2008
# Licensed under the GNU General Public License version 2 (June, 1991)
#
# Part of the R/eqtl package
# Contains: plotRsq
#
######################################################################
######################################################################
#
# plotRsq: histograms of R square values distribution
#
######################################################################
`plotRsq` <-
function(rsq, par=c(2,2), ...)
{
if ( ! any(class(rsq) == "rsq"))
stop("rsq should have class \"rsq\" \"data.frame\" .")
if ( !is.vector(par) & !is.integer(par) & length(par) != 2 )
stop("par is the mfrow parameter of the par() function. par should be a vector of 2 integers.")
interaction <- grep(':',rsq$qtl)
if ( ! length(interaction) > 0 ) par(mfrow=c(1,1))
else par(mfrow=par)
hist( as.numeric(as.vector(rsq$rsq)),
nclass=100,
xaxp=c(0,1,10),
main='',
ylab='Number of eQTLs and significant eQTL-eQTL interactions',
xlab='R square values',
...
)
if ( ! length(interaction) > 0 ) return('No qtl interaction detected')
hist( as.numeric(as.vector(rsq$rsq[-interaction])),
nclass=100,
xaxp=c(0,1,10),
main='',
ylab='Number of eQTLs',
xlab='R square values',
...
)
hist( as.numeric(as.vector(rsq$rsq[interaction])),
nclass=20,
xaxp=c(0,1,100),
main='',
ylab='Number of eQTL-eQTL interactions',
xlab='R square values',
...
)
}
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