R help - Aug 2010 - Lattice: Superimposing histograms with different colors and transparency effects

Dear users,

I would like to plot several histograms superimposed on the same panel
with different colors, with superimposed polygons appearing with
transparency effects. I also want estimated densities to appear on the
same plot. For several reasons, including that I like it, I want to use
the lattice package.

I have several questions regarding the use of the 'histogram' function
with a group structure.

I first thought that defining well-chosen values of alpha in trellis
parameters would give the transparency effets, but this is not the case:

library(lattice)

# Some data
x = c(rnorm(100), rnorm(100,2), rnorm(100,4))
grouping = gl(3,100,300)

# Trellis parameters
trellis.par.set("superpose.polygon"=list(alpha=rep(.5,3)))

histogram(~x ,groups=grouping, type = "density",
       panel = "panel.superpose",
       panel.groups = function(x,...) {
         panel.histogram(x,...)
         panel.mathdensity(dmath=dnorm,args list(mean=mean(x),sd=sd(x)),...)
       })

Besides transparency, I get no filling colors at all in the, even though
plot.polygon and superpose.polygon parameters are set. I clearly need to
define my own colors with alpha channel set:

mycolors = rgb(c(228, 55, 77), 
             c(26, 126, 175),
             c(28, 184, 74),alpha = 50,maxColorValue = 255)

... and include 'mycolors' as an explicit argument in the histogram
function:

histogram(~x ,groups=grouping, type = "density",ylim=c(0,.45),
       panel = "panel.superpose",col=mycolors,
       auto.key=list(space="right",rectangles=FALSE,col=mycolors),
       panel.groups = function(x,...) {
         panel.histogram(x,...)
         panel.mathdensity(dmath=dnorm,
args=list(mean=mean(x),sd=sd(x)),...)
       })

-> First question: Is it the only mean to get histogram bars filled, or
do I do something wrong in the use of trellis.arg.set ?

The problem with the previous approach is that the 'col' argument also
affects the density curves colors, for which I don't want transparency
effects. The 'col.lines' argument doesn't seem to change anything.
Removing the (...) arguments is not an interesting option, as it
suppresses some useful parameters for histograms (breaks, etc.).

-> Second question: How do I get superimposed density curves with colors
that differ from the bar colors (i.e. here: No transparency effects)?

-> Third question: How do I find nice (and common) ylim values for the
three histograms? I have set ylim=c(0,.45) above by hand, but I would
like to see this calibrated beforehand. Adding a prepanel function is
probably the way to go, but I am not sure how to manage this.

-> Fourth question: I would like the bar borders to have colors that
also vary from group to group, but unlike the 'col=' argument, adding a
'border=mycolors' argument in the histogram function call change colors
from bar to bar!

Thank you very much in advance.

Best wishes,

Yvonnick Noel, PhD.
University of Brittany, Rennes
France

Hi Yvonnick,

Have you looked at ggplot2?  There are two examples at the end of [1].

HTH,
Jorge

[1]  http://had.co.nz/ggplot2/geom_histogram.html



On Fri, Aug 13, 2010 at 4:12 PM, Yvonnick NOEL <> wrote:
> Dear users,
>
> I would like to plot several histograms superimposed on the same panel
> with different colors, with superimposed polygons appearing with
> transparency effects. I also want estimated densities to appear on the
> same plot. For several reasons, including that I like it, I want to use
> the lattice package.
>
> I have several questions regarding the use of the 'histogram'
function
> with a group structure.
>
> I first thought that defining well-chosen values of alpha in trellis
> parameters would give the transparency effets, but this is not the case:
>
> library(lattice)
>
> # Some data
> x = c(rnorm(100), rnorm(100,2), rnorm(100,4))
> grouping = gl(3,100,300)
>
> # Trellis parameters
> trellis.par.set("superpose.polygon"=list(alpha=rep(.5,3)))
>
> histogram(~x ,groups=grouping, type = "density",
>       panel = "panel.superpose",
>       panel.groups = function(x,...) {
>         panel.histogram(x,...)
>         panel.mathdensity(dmath=dnorm,args >
list(mean=mean(x),sd=sd(x)),...)
>       })
>
> Besides transparency, I get no filling colors at all in the, even though
> plot.polygon and superpose.polygon parameters are set. I clearly need to
> define my own colors with alpha channel set:
>
> mycolors = rgb(c(228, 55, 77),
>             c(26, 126, 175),
>             c(28, 184, 74),alpha = 50,maxColorValue = 255)
>
> ... and include 'mycolors' as an explicit argument in the histogram
> function:
>
> histogram(~x ,groups=grouping, type = "density",ylim=c(0,.45),
>       panel = "panel.superpose",col=mycolors,
>       auto.key=list(space="right",rectangles=FALSE,col=mycolors),
>       panel.groups = function(x,...) {
>         panel.histogram(x,...)
>         panel.mathdensity(dmath=dnorm,
> args=list(mean=mean(x),sd=sd(x)),...)
>       })
>
> -> First question: Is it the only mean to get histogram bars filled, or
> do I do something wrong in the use of trellis.arg.set ?
>
> The problem with the previous approach is that the 'col' argument
also
> affects the density curves colors, for which I don't want transparency
> effects. The 'col.lines' argument doesn't seem to change
anything.
> Removing the (...) arguments is not an interesting option, as it
> suppresses some useful parameters for histograms (breaks, etc.).
>
> -> Second question: How do I get superimposed density curves with colors
> that differ from the bar colors (i.e. here: No transparency effects)?
>
> -> Third question: How do I find nice (and common) ylim values for the
> three histograms? I have set ylim=c(0,.45) above by hand, but I would
> like to see this calibrated beforehand. Adding a prepanel function is
> probably the way to go, but I am not sure how to manage this.
>
> -> Fourth question: I would like the bar borders to have colors that
> also vary from group to group, but unlike the 'col=' argument,
adding a
> 'border=mycolors' argument in the histogram function call change
colors
> from bar to bar!
>
> Thank you very much in advance.
>
> Best wishes,
>
> Yvonnick Noel, PhD.
> University of Brittany, Rennes
> France
>
> ______________________________________________
> R-help@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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