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# Author : F.Rohart, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD
# created: 29-05-2014
# last modification: 10-10-2014
# Copyright (C) 2014
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
#-------------------------------------------
# Figure Supp. Stability
#-------------------------------------------
plot.bootsPLS=function(x,light,pch,col,legend.position,title, name.var = TRUE,...)
{
#name.var is either TRUE, FALSE, or a vector of length p
if(missing(x)) stop("`x' is missing")
H=ncol(x$nbr.var)
if(missing(light)) light=0
if(missing(pch)) pch=1:H
if(missing(col)) col=1:H
if(missing(legend.position)) legend.position="bottomright"
if(missing(title)) title="Frequency of selection depending on the component"
p=ncol(x$frequency)
if(light>0) #design to remove the variable that are never selected from the plot
{
ind=apply(x$frequency,2,function(x){sum(x>light)})#genes that are selected more than light on at least one component
ind=which(ind>0)
}else{ind=1:p}
ylab="Frequency"
#name.var
#-----
axis.label = FALSE
if(!is.logical(name.var))
{
if(length(name.var)!= (p+length(x$nzv$Position)))
stop("'name.var' should be a vector of length ", p+length(x$nzv$Position))
axis.label = TRUE
if(length(x$nzv$Position)>0)
name.var = name.var[-x$nzv$Position] #remove the variables that were removed by nzv
} else if (name.var){
name.var = substr(colnames(x$data$X),1,30)
axis.label = TRUE
}
if(axis.label == TRUE)
{
par(mar=c(10,4,4,2)+0.1)
plot(ind,x$frequency[1,ind],ylab=ylab,xlab="",pch=pch[1],col=col[1],xaxt="n",ylim=c(0,1),main=title,...)
axis(side=1,at=1:ncol(x$data$X),labels=name.var,las=2)
} else {
plot(ind,x$frequency[1,ind],ylab=ylab,xlab="",pch=pch[1],col=col[1],ylim=c(0,1),main=title,...)
}
for(i in c(1:H,1)) points(ind,x$frequency[i,ind],col=col[i],pch=pch[i],...)
if(legend.position!=FALSE)
legend(legend.position,legend=paste("Comp",1:H),pch=pch,col=col)
#legend(ncol(x$frequency)-2000,0.3,legend=paste("Comp",1:H),pch=pch,col=col)
}#end function plot.stability
# exple
# plot.stability(x$frequency)
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