[R] Use of colour in plots

Fri Sep 19 16:15:39 CEST 2008

Steve,

You want something like this:

library(ggplot2)
n <- 1000
dataset <- data.frame(x = round(rnorm(n), 2), y = round(rnorm(n), 1), z
= rnorm(n))
ggplot(dataset, aes(x = x, y = y, colour = factor(z > 1))) +
geom_point() + scale_colour_manual(values = c(alpha("red", 1/4),
"green"))

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 op 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: Steve Murray [mailto:smurray444 op hotmail.com] 
Verzonden: vrijdag 19 september 2008 16:01
Aan: ONKELINX, Thierry; r-help op r-project.org
Onderwerp: RE: [R] Use of colour in plots

Sorry - I should've maybe also pointed out that the command I've been
trying to use is: alpha(col="green", 1/10)

On its own this results in the following error: [1] "#00FF001A"  and I
haven't been able to successfully incorporate it into the main formula
just yet (please see my previous message).

Without wanting to get too far ahead of myself, is there also a way of
making the red points transparent too? (within this command - I've tried
using '&' but this results in an error).

Many thanks again for any advice you can offer,

Steve

> From: smurray444 op hotmail.com
> To: thierry.onkelinx op inbo.be; r-help op r-project.org
> Subject: RE: [R] Use of colour in plots
> Date: Fri, 19 Sep 2008 13:45:43 +0000
>
>
> Thierry,
>
> Thanks - I've had a look into using the transparency option, but can't
seem to work out where to place it within the command I'm using:
>
>> ggplot(Jan, aes(x = PopDensity, y = Average.Burnt.Area.Fraction,
colour = factor(Urban.Rural> 1.25))) + geom_point()
>
> I'm assuming that it has to go in the 'aes' section somewhere, but I
seem to be encountering errors wherever I insert it. This doesn't seem
to be mentioned in the book, so do you have any tips?!
>
> Also, out of interest, what does the 'geom_point()' command do?
>
> Thanks again,
>
> Steve
>
>
>
>> Subject: RE: [R] Use of colour in plots
>> Date: Fri, 19 Sep 2008 10:31:58 +0200
>> From: Thierry.ONKELINX op inbo.be
>> To: smurray444 op hotmail.com; r-help op r-project.org
>>
>> Steve,
>>
>> - Use tranparancy to prevent overplotting: more details on p. 16 of
the
>> ggplot2 book: http://had.co.nz/ggplot2/book/
>> - You can choose your own colour with scale_manual():
>> http://had.co.nz/ggplot2/scale_manual.html
>> - The backgroundcolor can be set with ggopt(background.color =
"white"):
>> http://rweb.stat.umn.edu/R/library/ggplot/html/build-options-8a.html
>>
>> 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 op 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: Steve Murray [mailto:smurray444 op hotmail.com]
>> Verzonden: donderdag 18 september 2008 19:08
>> Aan: r-help op r-project.org; ONKELINX, Thierry; petr.pikal op precheza.cz;
>> jrkrideau op yahoo.ca; jim op bitwrit.com.au
>> Onderwerp: RE: [R] Use of colour in plots
>>
>>
>> Dear Thierry and all,
>>
>> I've tried out ggplot from the ggplot2 package and it seems to
provide
>> much more favourable results!
>>
>> Just a few questions I have after consulting the 'help' file for
ggplot.
>>
>> Is there a way of preventing overplotting? Some of the red points are
>> being obscured by the green ones. I've tried changing the size of the
>> points (using size=1) but this doesn't resolve the issue, as there
are
>> many points quite densely packed in some parts of the graph.
>>
>> Also how would I change the colours if I wished (for future plots of
a
>> similar format)? And how do you customise the legend?
>>
>> Finally, is there a way of changing the grey background of the graph
to
>> white?
>>
>> Sorry for all the questions, it's just that I'm new to the ggplot2
>> package and can't find the answers in the help file or on the
associated
>> website!
>>
>> Many thanks to anyone who's able to offer any advice.
>>
>> Best wishes,
>>
>> Steve
>>
>>
>>
>>> Subject: RE: [R] Use of colour in plots
>>> Date: Thu, 18 Sep 2008 14:52:57 +0200
>>> From: Thierry.ONKELINX op inbo.be
>>> To: smurray444 op hotmail.com; petr.pikal op precheza.cz;
jrkrideau op yahoo.ca
>>> CC: r-help op r-project.org
>>>
>>> Steve,
>>>
>>> Have a look at the ggplot2 package:
>>>
>>> library(ggplot2)
>>> ggplot(Jan, aes(x = PopDensity, y = Average.Burnt.Area.Fraction,
>> colour
>>> = factor(Urban.Rural> 1.25))) + geom_point()
>>>
>>>
>>>
>>
------------------------------------------------------------------------
>>> ----
>>> 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 op 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 op r-project.org
>> [mailto:r-help-bounces op r-project.org]
>>> Namens Steve Murray
>>> Verzonden: donderdag 18 september 2008 13:58
>>> Aan: Petr PIKAL; jrkrideau op yahoo.ca
>>> CC: r-help op r-project.org
>>> Onderwerp: Re: [R] Use of colour in plots
>>>
>>>
>>> Dear all,
>>>
>>> I've finally got round to plotting my data and trying to apply
colour
>>> (had some problems with the data which I needed to rectify first!).
>> I'm
>>> having trouble however getting the colour to work as I'd hoped,
>> despite
>>> the help offered in previous messages.
>>>
>>> Just to recap, and with more specifics this time, I have a data
frame
>> as
>>> follows:
>>>
>>>
>>>> head(Jan)
>>> Latitude Longitude Urban.Rural Average.Burnt.Area.Fraction
PopDensity
>>> GDP
>>> 1 -0.25 -49.25 1.000000 9e-05 1.8703090
>>> 25694
>>> 2 -0.25 -50.25 1.000000 2e-05 2.5962470
>>> 32205
>>> 3 -0.25 -50.75 1.000000 0e+00 3.5221470
>>> 39312
>>> 4 -0.25 -51.25 1.042432 5e-06 14.2919000
>>> 87685
>>> 5 -0.25 -51.75 1.000000 1e-05 0.5721315
>>> 11376
>>> 6 -0.25 -52.25 1.000000 4e-05 0.7262031
>>> 11083
>>> Cropland.Area..km.2.grid.cell.
>>> 1 0.4260444
>>> 2 0.3401146
>>> 3 0.3036076
>>> 4 0.3147694
>>> 5 0.2843388
>>> 6 0.1734099
>>>
>>>
>>> I hope to plot Average.Burnt.Area.Fraction (ABAF) against PopDensity
>>> (which I have done using:> plot(Jan[,3],Jan[,4]) ).
>>>
>>> However, the twist is, I hope these points to be coloured according
to
>>> the values of Urban.Rural (but don't want this column to actually be
>>> plotted). I am looking to do, if Urban.Rural>1.25 then colour the
>> point
>>> red, and if it's = To: jrkrideau op yahoo.ca
>>>> CC: r-help op r-project.org; smurray444 op hotmail.com
>>>> Subject: Re: [R] Use of colour in plots
>>>> From: petr.pikal op precheza.cz
>>>> Date: Fri, 5 Sep 2008 16:40:47 +0200
>>>>
>>>> Hi
>>>>
>>>> r-help-bounces op r-project.org napsal dne 05.09.2008 16:24:35:
>>>>
>>>>> Here is an example doing the same type of thing.
>>>>> It should be easy enough to adapt.
>>>>>
>>>>> Good luck
>>>>>
>>>>> ===========================================================
>>>>> x <- runif(100, 0, 1)
>>>>> y <- runif(100, 0, 1)
>>>>> z <- data.frame(x,y)
>>>>>
>>>>> plot(subset(z, z$y>=.5), col="red", ylim=c(min(z$y),
>>>>> max(z$y)), pch=16)
>>>>> points(subset(z, z$y <=.49), col="blue", pch=16)
>>>>> ===========================================================
>>>>
>>>> Or
>>>>
>>>> third <- (z$y>=.5)+1
>>>> plot(z, col=third, pch=16)
>>>>
>>>> Just tell to col a vector of colors with appropriate use of
logical.
>>>>
>>>> Or you can use col = as.numeric(some factor), which is quite
>>> convenient
>>>> use of factors feature which is not desired in other cases.
>>>> See warning section of factor help page.
>>>>
>>>> Regards
>>>>
>>>>>
>>>>>
>>>>> --- On Fri, 9/5/08, Steve Murray wrote:
>>>>>
>>>>>> From: Steve Murray
>>>>>> Subject: [R] Use of colour in plots
>>>>>> To: r-help op r-project.org
>>>>>> Received: Friday, September 5, 2008, 9:10 AM
>>>>>> Dear all,
>>>>>>
>>>>>> I have 3 datasets all of which share the same longitude and
>>>>>> latitude values, which I'm looking to plot onto a
>>>>>> scattergraph. The third dataset has values which can only be
>>>>>> either '1' or '2'. So to incorporate all
>>>>>> three datasets onto two axes, I'm wondering if I can
>>>>>> plot dataset1 and dataset2 as normal, but then use colour to
>>>>>> determine whether these points are either values '1'
>>>>>> or '2' according to the third dataset.
>>>>>>
>>>>>> If so, how would I go about doing this in R, and what
>>>>>> format would the command take?
>>>>>>
>>>>>> Thanks for any help offered,
>>>>>>
>>>>>> Steve
>>>>>>
>>>>>> ______________________________________________
>>>>>> R-help op 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.
>>>>>
>>>>> ______________________________________________
>>>>> R-help op 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.
>>>>
>>>
>>> ______________________________________________
>>> R-help op 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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