Jan Verbesselt
2005-Aug-22 20:58 UTC
[R] How to add legend of plot.Design function (method=image)? (if (!.R.) )
Hi,
When running
z <- plot(fit, age=NA, cholesterol=NA, perim=boundaries,
method='image')
Legend(z, fun=plogis, at=qlogis(c(.01,.05,.1,.2,.3,.4,.5)),
zlab='Probability')
And after pointing the cursor to the plot() screen in R, I obtain the
following message:
Using function "locator(2)" to place opposite corners of image.legend
Error in Legend.plot.Design(z, fun = plogis, at = qlogis(c(0.01, 0.05, :
couldn't find function "subplot"
*How can I position the legend inside the range? (or solve the following
error message).
Regards,
Jan
-----Original Message-----
From: Jan Verbesselt [mailto:Jan.Verbesselt@biw.kuleuven.be]
Sent: Monday, August 22, 2005 4:59 PM
To: 'r-help@stat.math.ethz.ch'
Subject: How to add legend of plot.Design function ( method=image)?
Dear Rlist,
How can the Legend of the plot.Design() function can be visualized?
Following the documentation in R, I did the following (see below), only the
'Legend' function doesn't visualize the legend of the
plot (method='image') of the lrmfit. I tried to change par( margin
setting)
but this didn’t solve it.
How can this be solved?
Thanks a lot,
Jan
library(Design)
n <- 1000 # define sample size
set.seed(17) # so can reproduce the results
age <- rnorm(n, 50, 10)
blood.pressure <- rnorm(n, 120, 15)
cholesterol <- rnorm(n, 200, 25)
sex <- factor(sample(c('female','male'),
n,TRUE))
label(age) <- 'Age' # label is in Hmisc
label(cholesterol) <- 'Total Cholesterol'
label(blood.pressure) <- 'Systolic Blood Pressure'
label(sex) <- 'Sex'
units(cholesterol) <- 'mg/dl' # uses units.default in Hmisc
units(blood.pressure) <- 'mmHg'
# Specify population model for log odds that Y=1
L <- .4*(sex=='male') + .045*(age-50) +
(log(cholesterol - 10)-5.2)*(-2*(sex=='female') +
2*(sex=='male'))
# Simulate bin
ary y to have Prob(y=1) = 1/[1+exp(-L)]
y <- ifelse(runif(n) < plogis(L), 1, 0)
ddist <- datadist(age, blood.pressure, cholesterol, sex)
options(datadist='ddist')
fit <- lrm(y ~ blood.pressure + sex * (age + rcs(cholesterol,4)),
x=TRUE, y=TRUE)
boundaries <- perimeter(age, cholesterol, lowess=TRUE)
plot(age, cholesterol) # show bivariate data density
lines(boundaries) # and perimeter that will be used for 3-D plot
z <- plot(fit, age=NA, cholesterol=NA, perim=boundaries,
method='image')
# draws image() plot
# don't show estimates where data are sparse
# doesn't make sense here since vars don't
interact
if(!.R.)Legend(z, fun=plogis, at=qlogis(c(.01,.05,.1,.2,.3,.4,.5)),
zlab='Probability') # gray scale or color legend for prob.
_______________________________________________________________________
Ir. Jan Verbesselt
Research Associate
Group of Geomatics Engineering
Department Biosystems ~ M³-BIORES
Vital Decosterstraat 102, 3000 Leuven, Belgium
Tel: +32-16-329750 Fax: +32-16-329760
http://gloveg.kuleuven.ac.be/
_______________________________________________________________________
[[alternative HTML version deleted]]
Frank E Harrell Jr
2005-Aug-22 21:15 UTC
[R] How to add legend of plot.Design function (method=image)? (if (!.R.) )
Jan Verbesselt wrote:> Hi, > > > > When running > > > > z <- plot(fit, age=NA, cholesterol=NA, perim=boundaries, method='image') > > Legend(z, fun=plogis, at=qlogis(c(.01,.05,.1,.2,.3,.4,.5)), > zlab='Probability') > > > > And after pointing the cursor to the plot() screen in R, I obtain the > following message: > > > > Using function "locator(2)" to place opposite corners of image.legend > > Error in Legend.plot.Design(z, fun = plogis, at = qlogis(c(0.01, 0.05, : > > couldn't find function "subplot" > > > > *How can I position the legend inside the range? (or solve the following > error message). > > > > Regards, > > JanThe if(!.R.) in the example code was for a reason: I couldn't find subplot in R. If you want to provide code enhancements to do this I will incorporate your new code. -Frank> > > > > > > > -----Original Message----- > From: Jan Verbesselt [mailto:Jan.Verbesselt at biw.kuleuven.be] > Sent: Monday, August 22, 2005 4:59 PM > To: 'r-help at stat.math.ethz.ch' > Subject: How to add legend of plot.Design function ( method=image)? > > > > > > Dear Rlist, > > > > How can the Legend of the plot.Design() function can be visualized? > > > > Following the documentation in R, I did the following (see below), only the > 'Legend' function doesn't visualize the legend of the > > plot (method='image') of the lrmfit. I tried to change par( margin setting) > but this didn抰 solve it. > > > > How can this be solved? > > > > Thanks a lot, > > Jan > > > > > > library(Design) > > n <- 1000 # define sample size > > set.seed(17) # so can reproduce the results > > age <- rnorm(n, 50, 10) > > blood.pressure <- rnorm(n, 120, 15) > > cholesterol <- rnorm(n, 200, 25) > > sex <- factor(sample(c('female','male'), n,TRUE)) > > label(age) <- 'Age' # label is in Hmisc > > label(cholesterol) <- 'Total Cholesterol' > > label(blood.pressure) <- 'Systolic Blood Pressure' > > label(sex) <- 'Sex' > > units(cholesterol) <- 'mg/dl' # uses units.default in Hmisc > > units(blood.pressure) <- 'mmHg' > > > > # Specify population model for log odds that Y=1 > > L <- .4*(sex=='male') + .045*(age-50) + > > (log(cholesterol - 10)-5.2)*(-2*(sex=='female') + 2*(sex=='male')) > > # Simulate bin > > ary y to have Prob(y=1) = 1/[1+exp(-L)] > > y <- ifelse(runif(n) < plogis(L), 1, 0) > > > > ddist <- datadist(age, blood.pressure, cholesterol, sex) > > options(datadist='ddist') > > > > fit <- lrm(y ~ blood.pressure + sex * (age + rcs(cholesterol,4)), > > x=TRUE, y=TRUE) > > > > boundaries <- perimeter(age, cholesterol, lowess=TRUE) > > plot(age, cholesterol) # show bivariate data density > > lines(boundaries) # and perimeter that will be used for 3-D plot > > z <- plot(fit, age=NA, cholesterol=NA, perim=boundaries, method='image') > > # draws image() plot > > # don't show estimates where data are sparse > > # doesn't make sense here since vars don't > interact > > if(!.R.)Legend(z, fun=plogis, at=qlogis(c(.01,.05,.1,.2,.3,.4,.5)), > zlab='Probability') # gray scale or color legend for prob. > > > > _______________________________________________________________________ > Ir. Jan Verbesselt > Research Associate > Group of Geomatics Engineering > Department Biosystems ~ M伋-BIORES > Vital Decosterstraat 102, 3000 Leuven, Belgium > Tel: +32-16-329750 Fax: +32-16-329760 > http://gloveg.kuleuven.ac.be/ > _______________________________________________________________________ > > > > > [[alternative HTML version deleted]] > > > > ------------------------------------------------------------------------ > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html-- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University