[R] ggplot, qplot: alpha channel for colors corresponding to factor

ONKELINX, Thierry Thierry.ONKELINX at inbo.be
Wed Jun 10 14:02:40 CEST 2009


Dear Marianne,

If find that a bit easier with ggplot() instead of qplot()

d1 <- data.frame(Goodall=c(rep(1:3,5)), Better.adapt =
c(rep(1,7),rep(2,8)),Second.adapt=c(rep(1:5,3)))
library(ggplot2) 
ggplot(d1, aes(x= Goodall, y = Better.adapt, colour=Second.adapt)) +
geom_jitter(alpha = 0.2) + scale_colour_gradient(low = "white", high =
"black")

Another option would be to convert Second.adapt to a factor and use
scale_colour_manual

d1$Second <- factor(d1$Second.adapt)
ggplot(d1, aes(x= Goodall, y = Better.adapt, colour=Second)) +
geom_jitter(alpha = 0.9) + scale_colour_manual(values = c("white",
"grey", "black", "green", "red"))

HTH,

Thierry


------------------------------------------------------------------------
----
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature
and Forest
Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
methodology and quality assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium
tel. + 32 54/436 185
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 Marianne Promberger
Verzonden: woensdag 10 juni 2009 13:37
Aan: R-help
Onderwerp: [R] ggplot, qplot: alpha channel for colors corresponding to
factor

Hi,

I have a qplot like the one in the minimal example below, except I also
have faceting like this:

qplot(jitter(Goodall),jitter(Better.adapt),colour=Second.adapt,facets=~P
ol,data=d1)

and with the real data I get quite a lot of overplotting, so I would
like to add an alpha channel.

In addition, I would like to be able to control which colors are used
for each value of Second.adapt (which takes 7 different values). With my
original data, qplot by default uses a range from blue to red, which is
quite suitable, but I probably need to change this to shades of grey for
publication. 

I tried
qplot(jitter(Goodall),jitter(Better.adapt),colour=I(alpha(Second.adapt,1
/5)),facets=~Pol,data=d1)
but that does not give me what I want (There is no legend and I don't
think anything corresponds to the seven values of Second.adapt).

Minimal example:

Goodall <- c(rep(1:3,5))
Better.adapt <- c(rep(1,7),rep(2,8))
Second.adapt <- c(rep(1:5,3))
d1 <-
data.frame(Goodall=c(Goodall),Better.adapt=c(Better.adapt),Second.adapt=
c(Second.adapt))
library(ggplot2)
qplot(jitter(Goodall),jitter(Better.adapt),colour=Second.adapt,data=d1)
# follwoing doesn't work:
qplot(jitter(Goodall),jitter(Better.adapt),colour=I(alpha(Second.adapt,1
/5)),data=d1)

Thanks for any pointers,

Marianne





--
Marianne Promberger PhD
http://www.psych.upenn.edu/~mpromber
PGP/GnuPG public key ID 80AD9916

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