R help - Jun 2009 - 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=~Pol,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

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.adaptc(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

______________________________________________
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.

Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer 
en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is
door een geldig ondertekend document. The views expressed in  this message 
and any annex are purely those of the writer and may not be regarded as stating 
an official position of INBO, as long as the message is not confirmed by a duly 
signed document.