[R] ggplot2: using coord_trans for logit -> probability
Brian Diggs
brian.s.diggs at gmail.com
Thu Apr 17 20:35:07 CEST 2014
On 4/17/2014 5:44 AM, Michael Friendly wrote:
> I know I can do that. My example was just a toy version of a more
> complex graph I
> generate on the logit scale, and save as gg.
> I wanted to know if there was a way to transform it to the probability
> scale by using
>
> gg + coord_trans()
> with some suitable argument(s)
>
> for example, this *does* work to transform x -> log(x)
>
> gg + coord_trans(x="log")
>
> Reading the documentation in scales, I tried
>
> plogis_trans <- function () {
> probability_trans("logis")
> }
>
> but I get errors when I try to use it:
>
> > gg + coord_trans(y="plogis")
> Error in if (zero_range(range)) { : missing value where TRUE/FALSE needed
> In addition: Warning message:
> In qfun(x, ...) : NaNs produced
The logis distribution (q/p functions) is the inverse of the one that
you want for this transformation. As such, you need to set up a custom
transformation.
inverse_logit_trans <- trans_new("inverse logit",
transform = plogis,
inverse = qlogis)
gg + coord_trans(ytrans = inverse_logit_trans)
gg + scale_y_continuous(trans = inverse_logit_trans)
The difference between these is that coord_trans only transforms the
coordinate scale; it does not change the location of the breaks or the
labels associated with them. The trans argument in a scale, on the other
hand, determines appropriate breaks slightly differently but sill labels
them based on the data (not transformed) values.
There are two ways to get what you want: do the transformations in the
aesthetics, or create a break determining function for the custom
transformation which works on the transformed scale as well as forcing
the labeling on the transformed scale.
ggplot(pred, aes(x=Age, y=plogis(fit))) +
geom_line(size = 2) + theme_bw() +
geom_ribbon(aes(ymin = plogis(fit - 1.96 * se.fit),
ymax = plogis(fit + 1.96 * se.fit)), alpha = 0.2,
color = "transparent") +
labs(x = "Age", y = "Probability (Better)")
OR
library("functional")
inverse_logit_brks_trans <-
trans_new("inverse logit",
transform = plogis,
inverse = qlogis,
breaks = Compose(plogis, extended_breaks(), qlogis),
format = Compose(plogis, format_format()))
gg + coord_trans(ytrans = inverse_logit_brks_trans)
gg + scale_y_continuous(trans = inverse_logit_brks_trans)
Note that the coord_trans version of this second one ignores the breaks
and labels aspects of the defined transformation. You need to use the
latter (passing it to scale_y_continuous) to get the full effect of what
you showed in gg2.
> -Michael
>
> On 4/17/2014 6:23 AM, ONKELINX, Thierry wrote:
>> Dear Michael,
>>
>> You can use geom_smooth directly.
>>
>> ggplot(pred, aes(x = Age, y = Better)) + geom_smooth(method = "glm",
>> family = binomial)
>>
>> Best regards,
>>
>> Thierry
>>
>> ir. Thierry Onkelinx
>> Instituut voor natuur- en bosonderzoek / Research Institute for Nature
>> and Forest
>> team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
>> Kliniekstraat 25
>> 1070 Anderlecht
>> Belgium
>> + 32 2 525 02 51
>> + 32 54 43 61 85
>> Thierry.Onkelinx at inbo.be
>> www.inbo.be
>>
>> To call in the statistician after the experiment is done may be no
>> more than asking him to perform a post-mortem examination: he may be
>> able to say what the experiment died of.
>> ~ Sir Ronald Aylmer Fisher
>>
>> The plural of anecdote is not data.
>> ~ Roger Brinner
>>
>> The combination of some data and an aching desire for an answer does
>> not ensure that a reasonable answer can be extracted from a given body
>> of data.
>> ~ John Tukey
>>
>> -----Oorspronkelijk bericht-----
>> Van: r-help-bounces at r-project.org
>> [mailto:r-help-bounces at r-project.org] Namens Michael Friendly
>> Verzonden: donderdag 17 april 2014 4:03
>> Aan: R-help
>> Onderwerp: [R] ggplot2: using coord_trans for logit -> probability
>>
>> I'm trying to see if & how I can use coord_trans() with ggplot2 to
>> transform the Y axis of a plot on the logit scale to the probability
>> scale, as opposed to recalculating everything "manually" and
>> constructing a new plot.
>> Here is a simple example of the 'base' plot I'd like to transform:
>>
>> data(Arthritis, package="vcdExtra")
>> Arthritis$Better <- as.numeric(Arthritis$Improved > "None")
>> arth.logistic <- glm(Better ~ Age, data=Arthritis, family=binomial)
>>
>> # get fitted values on the logit scale
>> pred <- data.frame(Arthritis,
>> predict(arth.logistic, se.fit=TRUE))
>> library(ggplot2)
>> library(scales)
>> # plot on logit scale
>> gg <- ggplot(pred, aes(x=Age, y=fit)) +
>> geom_line(size = 2) + theme_bw() +
>> geom_ribbon(aes(ymin = fit - 1.96 * se.fit,
>> ymax = fit + 1.96 * se.fit,), alpha = 0.2, color =
>> "transparent") +
>> labs(x = "Age", y = "Log odds (Better)") gg
>>
>> Things I've tried that don't work:
>>
>> > gg + coord_trans(ytrans="logis")
>> Error in get(as.character(FUN), mode = "function", envir = envir) :
>> object 'logis_trans' of mode 'function' was not found > > gg +
>> coord_trans(ytrans=probability_trans("logis"))
>> Error in if (zero_range(range)) { : missing value where TRUE/FALSE
>> needed In addition: Warning message:
>> In qfun(x, ...) : NaNs produced
>> >
>>
>> Doing what I want "manually":
>>
>> # doing it manually
>> pred2 <- within(pred, {
>> prob <- plogis(fit)
>> lower <- plogis(fit - 1.96 * se.fit)
>> upper <- plogis(fit + 1.96 * se.fit)
>> })
>>
>>
>> gg2 <- ggplot(pred2, aes(x=Age, y=prob)) +
>> geom_line(size = 2) + theme_bw() +
>> geom_ribbon(aes(ymin = lower,
>> ymax = upper), alpha = 0.2, color = "transparent") +
>> labs(x = "Age", y = "Probability (Better)")
>> gg2
>>
>>
>>
>> --
>> Michael Friendly Email: friendly AT yorku DOT ca
>> Professor, Psychology Dept. & Chair, Quantitative Methods
>> York University Voice: 416 736-2100 x66249 Fax: 416 736-5814
>> 4700 Keele Street Web: http://www.datavis.ca
>> Toronto, ONT M3J 1P3 CANADA
>>
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>
>
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