On 06/13/2010 01:48 PM, beloitstudent wrote:
Hello all,
I have been having trouble getting a break in my y-axis. All of my data
points are up around 100-200, but the graph has to start at zero, so i would
like to remove all the white space using a break symbol. I have been able
to get the break and labels to be correct, however, I can't seem to get the
data to match the axis anymore. I must be using the axis.break() in plotrix
incorrectly, but I cannot see where my issue is. This is what I have so
far.
######
library(plotrix)
par(mar=c(6,8,4,4))
###Data
Saline<- structure(list(Time = c(-20L, 0, 30L, 45L, 60L, 80L,
110L,140L,200L, 260L, 320L), Average =
c(119.250,118.750,117.500,132.75,151.875,159.75,142.75,160,168,167.125,143),SEM=c(2.211,2.569,2.665,5.435146394,6.208741369,8.363550657,8.51349469,14.30284687,15.93865792,16.76541326,13.796)),
.Names = c("Time (min)", "Arterial Plasma Glucose (µg/mL)", "SEM"), class =
"data.frame", row.names = c("1", "2","3", "4", "5", "6", "7", "8", "9",
"10", "11"))
Ex<- structure(list(Time = c(-20L, 0, 30L, 45L, 60L, 80L, 110L,140L,200L,
260L, 320L), Average =
c(117.500,117.625,117.375,134.5,166.25,173.5,164.25,162.5,160.375,150.25,139.875),SEM
=
c(1.484614978,1.748906364,1.761,5.613395058,9.642063459,9.493284415,8.220804866,8.967059901,11.91626825,11.27169111,10.92915498)),
.Names = c("Time (min)", "Arterial Plasma Glucose (µg/mL)", "SEM"), class =
"data.frame", row.names = c("1", "2", "3", "4", "5", "6", "7", "8", "9",
"10", "11"))
####plotted data with error bars
plotCI(x=Saline [,1],y=Saline [,2], uiw=Saline [,3], err="y",
pt.bg=par("bg"),pch=19, cex=2.5 ,gap=0, sfrac=0.005,
xlim=c(-20,340),xaxp=c(-20,320,12), xlab="Time (min)",
ylim=c(0,200),yaxp=c(0,200,10), ylab="Arterial Plasma\nGlucose (µg/mL)",
las=1, axes=FALSE, font.lab=2.2,cex.lab=1.6)
plotCI(x=Ex [,1],y=Ex [,2], uiw=Ex [,3], err="y",pt.bg="white",pch=21,
col="black",cex=2.5 ,gap=0, sfrac=0.005, xlim=c(-20,340),xaxp=c(-20,320,12),
xlab="Time (min)", ylim=c(0,200), yaxp=c(0,200,10), ylab="Arterial
Plasma\nGlucose (µg/mL)", las=1, font.lab=2.2, axes=FALSE, add=TRUE,
cex.lab=1.9)
##########x-axis
axis(1, at=c("-20", "0", "30", "45", "60", "80", "110", "140", "200", "260",
"320"), lwd=2, font=2, pos=0,cex.axis=.9)
########y-axis
axis(2, las=1, at=c(0,40,60,80,100,120, 140), labels=c("0", "100", "120",
"140", "160", "180", "200"), lwd=2, font=2, pos="-20", cex.axis=1.7)
#####axis break
axis.break(2, 20, style="slash")
As you can see, my data does not fit my axis anymore. Any help with this
problem would be fantastic. Thanks!
Hi beloitstudent,
You have two problems here. First, if you want the plotted values to
match the offset labels on the y-axis, you are going to have to apply
the same offset to the y values.
plotCI(x=Saline [,1],y=Saline [,2]-60,...
plotCI(x=Ex [,1],y=Ex [,2]-60,...
The other problem is mine, I guess. I hadn't thought of offset axes when
writing axis.break, so I've added an argument for "pos" as in the axis
function. The modified function is attached, and will be in the next
version of plotrix. Thanks for bringing my attention to this.
Jim
# axis.break places a break marker at the position "breakpos"
# in user coordinates on the axis nominated - see axis().
axis.break<-function(axis=1,breakpos=NULL,pos=NA,bgcol="white",breakcol="black",
style="slash",brw=0.02) {
# get the coordinates of the outside of the plot
figxy<-par("usr")
# flag if either axis is logarithmic
xaxl<-par("xlog")
yaxl<-par("ylog")
# calculate the x and y offsets for the break
xw<-(figxy[2]-figxy[1])*brw
yw<-(figxy[4]-figxy[3])*brw
if(!is.na(pos)) figxy<-rep(pos,4)
# if no break position was given, put it just off the plot origin
if(is.null(breakpos))
breakpos<-ifelse(axis%%2,figxy[1]+xw*2,figxy[3]+yw*2)
if(xaxl && (axis == 1 || axis == 3)) breakpos<-log10(breakpos)
if(yaxl && (axis == 2 || axis == 4)) breakpos<-log10(breakpos)
# set up the "blank" rectangle (left, bottom, right, top)
switch(axis,
br<-c(breakpos-xw/2,figxy[3]-yw/2,breakpos+xw/2,figxy[3]+yw/2),
br<-c(figxy[1]-xw/2,breakpos-yw/2,figxy[1]+xw/2,breakpos+yw/2),
br<-c(breakpos-xw/2,figxy[4]-yw/2,breakpos+xw/2,figxy[4]+yw/2),
br<-c(figxy[2]-xw/2,breakpos-yw/2,figxy[2]+xw/2,breakpos+yw/2),
stop("Improper axis specification."))
# get the current setting of xpd
old.xpd<-par("xpd")
# don't cut the break off at the edge of the plot
par(xpd=TRUE)
# correct for logarithmic axes
if(xaxl) br[c(1,3)]<-10^br[c(1,3)]
if(yaxl) br[c(2,4)]<-10^br[c(2,4)]
if(style == "gap") {
if(xaxl) {
figxy[1]<-10^figxy[1]
figxy[2]<-10^figxy[2]
}
if(yaxl) {
figxy[3]<-10^figxy[3]
figxy[4]<-10^figxy[4]
}
# blank out the gap area and calculate the line segments
if(axis == 1 || axis == 3) {
rect(breakpos,figxy[3],breakpos+xw,figxy[4],col=bgcol,border=bgcol)
xbegin<-c(breakpos,breakpos+xw)
ybegin<-c(figxy[3],figxy[3])
xend<-c(breakpos,breakpos+xw)
yend<-c(figxy[4],figxy[4])
if(xaxl) {
xbegin<-10^xbegin
xend<-10^xend
}
}
else {
rect(figxy[1],breakpos,figxy[2],breakpos+yw,col=bgcol,border=bgcol)
xbegin<-c(figxy[1],figxy[1])
ybegin<-c(breakpos,breakpos+yw)
xend<-c(figxy[2],figxy[2])
yend<-c(breakpos,breakpos+yw)
if(xaxl) {
xbegin<-10^xbegin
xend<-10^xend
}
}
# clip the lines
par(xpd=TRUE)
}
else {
# draw the "blank" rectangle
rect(br[1],br[2],br[3],br[4],col=bgcol,border=bgcol)
if(style == "slash") {
# calculate the slash ends
if(axis == 1 || axis == 3) {
xbegin<-c(breakpos-xw,breakpos)
xend<-c(breakpos,breakpos+xw)
ybegin<-c(br[2],br[2])
yend<-c(br[4],br[4])
if(xaxl) {
xbegin<-10^xbegin
xend<-10^xend
}
}
else {
xbegin<-c(br[1],br[1])
xend<-c(br[3],br[3])
ybegin<-c(breakpos-yw,breakpos)
yend<-c(breakpos,breakpos+yw)
if(yaxl) {
ybegin<-10^ybegin
yend<-10^yend
}
}
}
else {
# calculate the zigzag ends
if(axis == 1 || axis == 3) {
xbegin<-c(breakpos-xw/2,breakpos-xw/4,breakpos+xw/4)
xend<-c(breakpos-xw/4,breakpos+xw/4,breakpos+xw/2)
ybegin<-c(ifelse(yaxl,10^figxy[3+(axis==3)],figxy[3+(axis==3)]),br[4],br[2])
yend<-c(br[4],br[2],ifelse(yaxl,10^figxy[3+(axis==3)],figxy[3+(axis==3)]))
if(xaxl) {
xbegin<-10^xbegin
xend<-10^xend
}
}
else {
xbegin<-c(ifelse(xaxl,10^figxy[1+(axis==4)],figxy[1+(axis==4)]),br[1],br[3])
xend<-c(br[1],br[3],ifelse(xaxl,10^figxy[1+(axis==4)],figxy[1+(axis==4)]))
ybegin<-c(breakpos-yw/2,breakpos-yw/4,breakpos+yw/4)
yend<-c(breakpos-yw/4,breakpos+yw/4,breakpos+yw/2)
if(yaxl) {
ybegin<-10^ybegin
yend<-10^yend
}
}
}
}
# draw the segments
segments(xbegin,ybegin,xend,yend,col=breakcol,lty=1)
# restore xpd
par(xpd=FALSE)
}
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