Use of colour in plots

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

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Use of colour in plots

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