geom_smooth()

[Henri-Paul Indiogine]

Greetings!

I am getting more comfortable in using ggplot2 and prefer it above any
other plotting library in R-project. Thanks for this wonderful tool.

I am using geom_smooth() for my scatter charts using geom_point().
I would like a trend line added to the scattered points and use:

geom_smooth(aes(color = factor(variable)), se = FALSE)

I have many points with value = zero and thus I have noticed that the
line goes sometimes below the x-axis. All my data are positive
integers and thus a trend line in negative territory does not make
sense.

Could this be fixed? I looked into the stat_smooth() documentation,
but could find anything about it. By default it uses the "loess"
method. Do I need to change that or do I need to pass any parameters?

Thanks in advance and best regards,

Henri


--
Henri-Paul Indiogine

Curriculum & Instruction
Texas A&M University
TutorFind Learning Centre
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Email: hindi...@gmail.com
Skype: hindiogine

[Ben Bond-Lamberty]

Henri-Paul,

Providing a reproducible example will generally get you better answers, but...

If the smoothing function isn't behaving how you want, you can try a
different one--for example, geom_smooth(method="lm")--or provide your
own 'better-behaved' function, i.e. one that provides a better model
of whatever process is producing your data. The geom_smooth help page
gives an example of this, I believe.

Ben

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[ONKELINX, Thierry]

Are the values counts (= positive integers)? In that case a poisson regression is more suitable as smoother. E.g. geom_smooth(method = 'glm', family = 'poisson')

set.seed(12345)
library(ggplot2)
library(mgcv)
Dataset <- data.frame(A = seq(-10, 10, length = 1001))
Dataset$B <- rpois(nrow(Dataset), exp(2 + 0.1 * Dataset$A - 0.1 * Dataset$A ^ 2))
ggplot(Dataset, aes(x = A, y = B)) + geom_point() + geom_smooth()
ggplot(Dataset, aes(x = A, y = B)) + geom_point() + geom_smooth(method = "glm", family = "poisson")
ggplot(Dataset, aes(x = A, y = B)) + geom_point() + geom_smooth(method = "glm", family = "poisson", formula = y ~ poly(x, 2))
ggplot(Dataset, aes(x = A, y = B)) + geom_point() + geom_smooth(method = "gam", family = "poisson")
ggplot(Dataset, aes(x = A, y = B)) + geom_point() + geom_smooth(method = "gam", family = "poisson", formula = y ~ s(x))

ggplot(Dataset, aes(x = A, y = B)) + geom_smooth(method = "gam", family = "poisson", formula = y ~ s(x)) + coord_cartesian(ylim = (c(-0.1, 1))) #note that even the confidence intervals are non-negative

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....@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: ggp...@googlegroups.com [mailto:ggp...@googlegroups.com] Namens Henri-Paul Indiogine
Verzonden: woensdag 17 oktober 2012 19:31
Aan: ggp...@googlegroups.com
Onderwerp: geom_smooth()

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[Henri-Paul Indiogine]

Thierry, bedankt voor the suggesties.

Beste,
Henk (a.k.a. Henri)

2012/10/18 ONKELINX, Thierry <Thierry....@inbo.be>: