[R] Use of colour in plots

Fri Sep 19 18:14:01 CEST 2008

Hi Thierry and all,

Thanks very much for your suggestion. I've given it a go and played around with the transparency values, but seem to be having a problem in that some of the red values are made transparent, even though there are no green values being overplotted!

The code I used to display the image was:

ggplot(Jan, aes(x = Jan[,4], y = Jan[,5], colour = factor(Jan$Urban.Rural> 1.25))) +
geom_point() + scale_colour_manual(values = c(alpha("red",1/10),
"green"))

Do you have any ideas to put me on the right tracks with this?

Thanks again for your help,

Steve

> Subject: RE: [R] Use of colour in plots
> Date: Fri, 19 Sep 2008 16:15:39 +0200
> From: Thierry.ONKELINX at inbo.be
> To: smurray444 at hotmail.com; r-help at r-project.org
>
> 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 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: Steve Murray [mailto:smurray444 at hotmail.com]
> Verzonden: vrijdag 19 september 2008 16:01
> Aan: ONKELINX, Thierry; r-help at 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 at hotmail.com
>> To: thierry.onkelinx at inbo.be; r-help at 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 at inbo.be
>>> To: smurray444 at hotmail.com; r-help at 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 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: Steve Murray [mailto:smurray444 at hotmail.com]
>>> Verzonden: donderdag 18 september 2008 19:08
>>> Aan: r-help at r-project.org; ONKELINX, Thierry; petr.pikal at precheza.cz;
>>> jrkrideau at yahoo.ca; jim at 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 at inbo.be
>>>> To: smurray444 at hotmail.com; petr.pikal at precheza.cz;
> jrkrideau at yahoo.ca
>>>> CC: r-help at 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 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 Steve Murray
>>>> Verzonden: donderdag 18 september 2008 13:58
>>>> Aan: Petr PIKAL; jrkrideau at yahoo.ca
>>>> CC: r-help at 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 at yahoo.ca
>>>>> CC: r-help at r-project.org; smurray444 at hotmail.com
>>>>> Subject: Re: [R] Use of colour in plots
>>>>> From: petr.pikal at precheza.cz
>>>>> Date: Fri, 5 Sep 2008 16:40:47 +0200
>>>>>
>>>>> Hi
>>>>>
>>>>> r-help-bounces at 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 at 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 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.
>>>>>>
>>>>>> ______________________________________________
>>>>>> 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.
>>>>>
>>>>
>>>> ______________________________________________
>>>> 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.
>>>>
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