[R] smoothScatter plot
John Kane
jrkrideau at inbox.com
Fri Oct 5 16:36:38 CEST 2012
In line
John Kane
Kingston ON Canada
-----Original Message-----
From: zhyjiang2006 at hotmail.com
Sent: Fri, 5 Oct 2012 05:41:29 +0800
To: jrkrideau at inbox.com
Subject: RE: [R] smoothScatter plot
Hi John,
Thanks for your email. Your way works good.
However, I was wondering if you can help with a smoothed scatter plot that
has shadows with different darker blue color representing higher density of
points.
Zhengyu
Do you mean something like what is being discussed here?
http://andrewgelman.com/2012/08/graphs-showing-uncertainty-using-lighter-int
ensities-for-the-lines-that-go-further-from-the-center-to-de-emphasize-the-e
dges/
If so I think there has been some discussion and accompanying ggplot2 code
on google groups ggplot2 site.
Otherwise can you explain a bit more clearly?
_________________________________________________________________
Date: Thu, 4 Oct 2012 05:46:46 -0800
From: jrkrideau at inbox.com
Subject: RE: [R] smoothScatter plot
To: zhyjiang2006 at hotmail.com
CC: r-help at r-project.org
Hi,
Do you mean something like this?
=============================================
scatter.smooth(x,y)scatter.smooth(x,y)
=============================================
It looks like invoking that dcols <- densCols(x,y) is callling in some
package that is masking the basic::smoothScatter() and applying some other
version of smoothScatter, but I am not expert enough to be sure.
Another way to get the same result as mine with smoothScatter is to use the
ggplot2 package. it looks a bit more complicated but it is very good and in
some ways easier to see exactly what is happening.
To try it you would need to install the ggplot2 package
(install.packages("ggplot2") then with your original x and y data frames
===============================================
library(ggplot2)
xy <- cbind(x, y)
names(xy) <- c("xx", "yy")
p <- ggplot(xy , aes(xx, yy )) + geom_point( ) +
geom_smooth( method="loess", se =FALSE)
p
================================================
Thanks for the data set. However it really is easier to use dput()
To use dput() simply issue the command dput(myfile) where myfile is the file
you are working with. It will give you something like this:
======================================================
1> dput(x)
structure(c(0.4543462924, 0.2671718761, 0.1641577016, 1.1593356462,
0.0421177346, 0.3127782861, 0.4515537795, 0.5332559665, 0.0913911528,
0.1472054054, 0.1340672893, 1.2599304224, 0.3872026125, 0.0368560053,
0.0371828779, 0.3999714282, 0.0175815783, 0.8871547761, 0.2706762487,
0.7401904063, 0.0991320236, 0.2565567348, 0.5854167363, 0.7515717421,
0.7220388222, 1.3528297744, 0.9339971349, 0.0128652431, 0.4102527051
), .Dim = c(29L, 1L), .Dimnames = list(NULL, "V1"))
1> dput(y)
structure(list(V1 = c(0.8669898448, 0.6698647266, 0.1641577016,
0.4779091929, 0.2109900366, 0.2915241414, 0.2363116664, 0.3808731568,
0.379908928, 0.2565868263, 0.1986675964, 0.7589866876, 0.6496236922,
0.1327986663, 0.4196107999, 0.3436442638, 0.1910728051, 0.5625817464,
0.1429791079, 0.6441837334, 0.1477153617, 0.369079266, 0.3839842979,
0.39044223, 0.4186374286, 0.7611640016, 0.446291999, 0.2943343355,
0.3019098386)), .Names = "V1", class = "data.frame", row.names = c(NA,
-29L))
1>
=======================================================
That is your x in dput() form. You just copy it from the R terminal and
paste it into your email message. It is handy if you add the x <- and y
<- to the output.
Your method works just fine but it's a bit more cumbersome with a lot of
data.
Also, please reply to the R-help list as well. It is a source of much more
expertise than me and it also can reply when a single person is unavailable.
I hope this helps
John Kane
Kingston ON Canada
-----Original Message-----
From: zhyjiang2006 at hotmail.com
Sent: Thu, 4 Oct 2012 05:19:14 +0800
To: jrkrideau at inbox.com
Subject: RE: [R] smoothScatter plot
Hi John,
Thanks for your reply. But I cannot figure out how to use dput(). I included
data and code below. Is that possible to make a plot similar to attached
smoothing effect.
Zhengyu
###########
x<-read.table(text="0.4543462924
0.2671718761
0.1641577016
1.1593356462
0.0421177346
0.3127782861
0.4515537795
0.5332559665
0.0913911528
0.1472054054
0.1340672893
1.2599304224
0.3872026125
0.0368560053
0.0371828779
0.3999714282
0.0175815783
0.8871547761
0.2706762487
0.7401904063
0.0991320236
0.2565567348
0.5854167363
0.7515717421
0.7220388222
1.3528297744
0.9339971349
0.0128652431
0.4102527051",header=FALSE)
y<-read.table(text="0.8669898448
0.6698647266
0.1641577016
0.4779091929
0.2109900366
0.2915241414
0.2363116664
0.3808731568
0.379908928
0.2565868263
0.1986675964
0.7589866876
0.6496236922
0.1327986663
0.4196107999
0.3436442638
0.1910728051
0.5625817464
0.1429791079
0.6441837334
0.1477153617
0.369079266
0.3839842979
0.39044223
0.4186374286
0.7611640016
0.446291999
0.2943343355
0.3019098386",header=FALSE)
x<-data.matrix(x)
y<-data.matrix(y)
dcols <- densCols(x,y)
smoothScatter(x,y, col = dcols, pch=20,xlab="A",ylab="B")
################################
> Date: Tue, 2 Oct 2012 05:19:27 -0800
> From: jrkrideau at inbox.com
> Subject: RE: [R] smoothScatter plot
> To: zhyjiang2006 at hotmail.com; r-help at r-project.org
>
> It's hard to know what's wrong with your code since you did not supply it.
>
> Please supply a small working example and some data. To supply data use
the dput() function, see ?dput() for details.
>
> John Kane
> Kingston ON Canada
>
>
> > -----Original Message-----
> > From: zhyjiang2006 at hotmail.com
> > Sent: Tue, 2 Oct 2012 11:38:31 +0800
> > To: r-help at r-project.org
> > Subject: [R] smoothScatter plot
> >
> >
> >
> >
> >
> > Hi, I want to make a plot similar to sm1 (attached). The code I tried
is:
> > dcols <- densCols(x,y)
> > smoothScatter(x,y, col = dcols, pch=20,xlab="A",ylab="B")
> > abline(h=0, col="red")
> > But it turned out to be s1 (attached) with big dots. I was wondering if
> > anything wrong with my code. Thanks,Zhengyu
> > ______________________________________________
> > 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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