[R] How to add lines to lattice plot produced by rms::bplot
Frank Harrell
f.harrell at vanderbilt.edu
Sat Aug 14 15:59:26 CEST 2010
Once you guys figure all this out, I'm glad to modify bplot to pass
more arguments lattice if needed.
Frank E Harrell Jr Professor and Chairman School of Medicine
Department of Biostatistics Vanderbilt University
On Fri, 13 Aug 2010, David Winsemius wrote:
>
> On Aug 13, 2010, at 11:25 PM, Duncan Mackay wrote:
>
>> Hi David
>>
>> I do not know if you have done something like this.
>
> I had tried a few efforts like that, starting with an examination of
> str(bp.plot) as you demonstrate.
>
>> I tried str(bp.plot) which gave the section about the regions (for
>> colours) as:
>> $ panel.args.common:List of 8
>> ..$ x : num [1:2500] 27 28 29 29.9 30.9 ...
>> ..$ y : num [1:2500] 141 141 141 141 141 ...
>> ..$ z : num [1:2500] -1.43 -1.41 -1.39 -1.36 -1.34 ...
>> ..$ at : num [1:10] -2 -1.5 -1 -0.5 0 0.5 1 1.5 2 2.5
>> ..$ region : logi FALSE
>> ..$ zlab :List of 3
>> .. ..$ label: chr "log odds"
>> .. ..$ rot : num 90
>> .. ..$ cex : num 1
>> ..$ labels : logi TRUE
>> ..$ contour: logi TRUE
>
> I tried (with a bplot object named "bldLT40"):
>
> bldLT40$legend$right$args$key$at <- c(-0.233, seq(.50, 2.25, by=0.25),
> seq(2.5, 5.0, by=0.5), 6:10)
>
> ... and then tried
>
> bldLT40$panel.args$at <- c(-0.233, seq(.50, 2.25, by=0.25), seq(2.5,
> 5.0, by=0.5), 6:10)
>
> Neither of these efforts changed the boundaries beteen colors in the
> plot area. The first effort changed the legend scal,e but that just
> created a "misalignment" of the colors of plot area and the legend. I
> would be interested in either a strategy that lets one alter the color
> level changes of the z variable (which in bplot-created objects is
> "zhat", or lets one specify the values at which contour lines are
> drawn in contourplot.
>
> Thanks for your efforts.
>
> --
> David.
>
>
>>
>> I added the col.region and colours from a plot levelplot that I had
>> done to see what would occur to the trellis parameters. No colours
>> were produced when plotted.
>> bp.plot <- bplot(p, lfun=contourplot, color.key = TRUE, col.regions
>> =
>> c
>> ("#FFFFFF
>> ","#00FFFF","#A9E2FF","#8080FF","#0000FF","#FFD18F","#FF0000") )
>>
>> $ panel.args.common:List of 10
>> ..$ x : num [1:2500] 27 28 29 29.9 30.9 ...
>> ..$ y : num [1:2500] 141 141 141 141 141 ...
>> ..$ z : num [1:2500] -1.43 -1.41 -1.39 -1.36 -1.34 ...
>> ..$ at : num [1:10] -2 -1.5 -1 -0.5 0 0.5 1 1.5 2 2.5
>> ..$ region : logi FALSE
>> ..$ color.key : logi TRUE
>> ..$ zlab :List of 3
>> .. ..$ label: chr "log odds"
>> .. ..$ rot : num 90
>> .. ..$ cex : num 1
>> ..$ labels : logi TRUE
>> ..$ contour : logi TRUE
>> ..$ col.regions: chr [1:7] "#FFFFFF" "#00FFFF" "#A9E2FF"
>> "#8080FF" ...
>>
>> So it has been added to the panel.args.common, whether you can
>> access these are another matter.
>>
>> I then tried
>> bp.plot <- bplot(p, lfun=contourplot, par.settings = list(axis.text
>> = list(cex = 0.65)), color.key = TRUE, col.regions =
>> c
>> ("#FFFFFF
>> ","#00FFFF","#A9E2FF","#8080FF","#0000FF","#FFD18F","#FF0000") )
>>
>> which changed the size of the axis text so it may be the case of
>> having to add the col.regions etc to the appropriate list in
>> par.settings
>>
>> I'll leave you to amend and access the colours.
>> You may have to add values for the wireframe/levelplot arguments
>> like "at" etc. and col.regions (I think that is the function) to
>> produce an appropriate colour range of your choice
>>
>> It is a while since I have delved into these sorts of plots.
>> Need some sustenance.
>>
>> Regards
>>
>> Duncan
>>
>> Duncan Mackay
>> Department of Agronomy and Soil Science
>> University of New England
>> ARMIDALE NSW 2351
>> Email home: mackay at northnet.com.au
>>
>>
>>
>> At 10:33 14/08/2010, you wrote:
>>
>>> I have a plot produced by function bplot (package = rms) that is
>>> really a lattice plot (class="trellis"). It is similar to this plot
>>> produced by a very minor modification of the first example on the
>>> bplot help page:
>>>
>>> require(rms)
>>> 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 binary 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)
>>> p <- Predict(fit, age, cholesterol, sex='male', np=50) # vary sex
>>> last
>>> bp.plot <- bplot(p, lfun=contourplot)
>>> bp.plot
>>>
>>> I have tried a variety of efforts at using update (which I assume
>>> is a
>>> lattice function although I can find no help page for it. It does
>>> appear in some of the lattice hep pages and my understanding is that
>>> it pushes objects onto the list structure of a plot object. I've also
>>> tried adding to it with llines()
>>> #-------------
>>> Oh, never mind. I recovered a memory that I had seen a solution on
>>> rhelp and had saved it. Turns out it was from Peter Ehlers, to whom I
>>> offer thanks. I was trying to add a step function: ht and weight from
>>> a dataframe, "bld":
>>>
>>> trellis.focus("panel", 1, 1)
>>> panel.lines(x=bld$inches, y=bld$BMI28, type='s')
>>> trellis.unfocus()
>>>
>>> Success!
>>>
>>> Now... how do I control the color levels in levelplot or
>>> contourplot???
>>>
>>>
>>> David Winsemius, MD
>>> West Hartford, CT
>>>
>>> ______________________________________________
>>> R-help at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> David Winsemius, MD
> West Hartford, CT
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
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