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 -------------- next part -------------- A non-text attachment was scrubbed... Name: sm1.png Type: image/png Size: 23046 bytes Desc: not available URL: <https://stat.ethz.ch/pipermail/r-help/attachments/20121002/13c293ba/attachment-0004.png> -------------- next part -------------- A non-text attachment was scrubbed... Name: s1.png Type: image/png Size: 17877 bytes Desc: not available URL: <https://stat.ethz.ch/pipermail/r-help/attachments/20121002/13c293ba/attachment-0005.png>
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.____________________________________________________________ FREE ONLINE PHOTOSHARING - Share your photos online with your friends and family! Visit http://www.inbox.com/photosharing to find out more!
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.
>
> ____________________________________________________________
> FREE ONLINE PHOTOSHARING - Share your photos online with your friends
and
family!
> Visit http://www.inbox.com/photosharing to find out more!
>
>
_________________________________________________________________
Free Online Photosharing - Share your photos online with your friends and
family!
Visit [1]http://www.inbox.com/photosharing to find out more!
References
1. http://www.inbox.com/photosharing
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.
>
> ____________________________________________________________
> FREE ONLINE PHOTOSHARING - Share your photos online with your friends
and
family!
> Visit http://www.inbox.com/photosharing to find out more!
>
>
_________________________________________________________________
Free Online Photosharing - Share your photos online with your friends and
family!
Visit [1]http://www.inbox.com/photosharing to find out more!
_________________________________________________________________
[2]3D Marine Aquarium Screensaver Preview
Free 3D Marine Aquarium Screensaver
Watch dolphins, sharks & orcas on your desktop! Check it out at
[3]www.inbox.com/marineaquarium
References
1. http://www.inbox.com/photosharing
2. http://www.inbox.com/marineaquarium
3. http://www.inbox.com/marineaquarium
Hi Zhengyu,
You might want to have a look at
http://gallery.r-enthusiasts.com/graph/Scatterplots_with_smoothed_densities_color_representation,139
which seems to be showing a smoothScatter() that seems like what you want.?
I've never used the? function so I am probably not much help
Something else that I thought of, late yesterday, was the ggplot2 approach shown
using this code.?
d <- ggplot(diamonds, aes(carat, price))
d + geom_point()? # graph all points with similar colour
d + geom_point(alpha = 1/10)? # graph points with transparency setting
The alpha settings may give you something similar to smoothScatter() but
probably without the colours though a question on the google groups ggplot2
group might help.
Good luck
Good luck,
John Kane
Kingston ON Canada
-----Original Message-----
From: zhyjiang2006 at hotmail.com
Sent: Sat, 6 Oct 2012 01:01:41 +0800
To: jrkrideau at inbox.com
Subject: RE: [R] smoothScatter plot
Hi John,
Thanks for your link. Those plots?look pretty but way too complicated in terms
of making R code.?
Maybe my decription is not clear.? But could you take a look at the attached
png? I saw several publications showing smoothed plots like this but not sure
how to make one...
Thanks,
Best,
Zhengyu
Date: Fri, 5 Oct 2012 06:36:38 -0800
From: jrkrideau at inbox.com
Subject: RE: [R] smoothScatter plot
To: zhyjiang2006 at hotmail.com
CC: r-help at r-project.org
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-intensities-for-the-lines-that-go-further-from-the-center-to-de-emphasize-the-edges/
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.
>
> ____________________________________________________________
> FREE ONLINE PHOTOSHARING - Share your photos online with your friends and
family!
> Visit http://www.inbox.com/photosharing to find out more!
>
>
Free Online Photosharing - Share your photos online with your friends and
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find out more!
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Hi John,I installed & but somehow it did not work on my computer, while I
tried another computer - it works.
Thanks for all your communications.Best,Zhengyu
Date: Tue, 9 Oct 2012 05:16:59 -0800
From: jrkrideau@inbox.com
Subject: RE: [R] smoothScatter plot
To: zhyjiang2006@hotmail.com
Glad it helps a bit. I don't use such graphs so I'm not a good source of
information on them.
Re: the ggplot graph you need to load the ggplor2 library and probably this
means that you will have to install the ggplot2 package.
install.packages("ggplot2")
Then run this
library(ggplot2)
d <- ggplot(diamonds, aes(carat, price))
d + geom_point() # graph all points with similar colour
d + geom_point(alpha = 1/10) # graph points with transparency setting
Best of luck
John Kane
Kingston ON Canada
-----Original Message-----
From: zhyjiang2006@hotmail.com
Sent: Mon, 8 Oct 2012 22:46:35 +0800
To: jrkrideau@inbox.com
Subject: RE: [R] smoothScatter plot
Hi John,
Thanks a lot! One of figures in your link looks a lotof like what I want. I
guess geneplotter from bioconductor helps.
For ggplot2 package, was it the correct package for your code. There is always
an "Error: could not find function "ggplot"
Zhengyu > Date: Sat, 6 Oct 2012 08:00:20 -0800> From: jrkrideau@inbox.com
> Subject: RE: [R] smoothScatter plot
> To: zhyjiang2006@hotmail.com
> CC: r-help@r-project.org
>
> Hi Zhengyu,
>
> You might want to have a look at
http://gallery.r-enthusiasts.com/graph/Scatterplots_with_smoothed_densities_color_representation,139
> which seems to be showing a smoothScatter() that seems like what you want.
>
> I've never used the function so I am probably not much help
>
> Something else that I thought of, late yesterday, was the ggplot2 approach
shown using this code.
> d <- ggplot(diamonds, aes(carat, price))
> d + geom_point() # graph all points with similar colour
> d + geom_point(alpha = 1/10) # graph points with transparency setting
>
> The alpha settings may give you something similar to smoothScatter() but
probably without the colours though a question on the google groups ggplot2
group might help.
>
> Good luck
>
> Good luck,
>
> John Kane
> Kingston ON Canada
>
> -----Original Message-----
> From: zhyjiang2006@hotmail.com
> Sent: Sat, 6 Oct 2012 01:01:41 +0800
> To: jrkrideau@inbox.com
> Subject: RE: [R] smoothScatter plot
>
> Hi John,
>
> Thanks for your link. Those plots look pretty but way too complicated in
terms of making R code.
>
> Maybe my decription is not clear. But could you take a look at the
attached png? I saw several publications showing smoothed plots like this but
not sure how to make one...
>
> Thanks,
> Best,
> Zhengyu
>
> Date: Fri, 5 Oct 2012 06:36:38 -0800
> From: jrkrideau@inbox.com
> Subject: RE: [R] smoothScatter plot
> To: zhyjiang2006@hotmail.com
> CC: r-help@r-project.org
>
> In line
>
> John Kane
> Kingston ON Canada
>
> -----Original Message-----
> From: zhyjiang2006@hotmail.com
> Sent: Fri, 5 Oct 2012 05:41:29 +0800
> To: jrkrideau@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-intensities-for-the-lines-that-go-further-from-the-center-to-de-emphasize-the-edges/
>
> 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@inbox.com
> Subject: RE: [R] smoothScatter plot
> To: zhyjiang2006@hotmail.com
> CC: r-help@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@hotmail.com
> Sent: Thu, 4 Oct 2012 05:19:14 +0800
> To: jrkrideau@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@inbox.com
> > Subject: RE: [R] smoothScatter plot
> > To: zhyjiang2006@hotmail.com; r-help@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@hotmail.com
> > > Sent: Tue, 2 Oct 2012 11:38:31 +0800
> > > To: r-help@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@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.
> >
> > ____________________________________________________________
> > FREE ONLINE PHOTOSHARING - Share your photos online with your friends
and family!
> > Visit http://www.inbox.com/photosharing to find out more!
> >
> >
>
> Free Online Photosharing - Share your photos online with your friends and
family!
> Visit http://www.inbox.com/photosharing
[http://www.inbox.com/photosharing] to find out more!
>
> [http://www.inbox.com/marineaquarium]
> Free 3D Marine Aquarium Screensaver
> Watch dolphins, sharks & orcas on your desktop! Check it out at
www.inbox.com/marineaquarium [http://www.inbox.com/marineaquarium]
>
> ____________________________________________________________
> FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop!
> Check it out at http://www.inbox.com/earth
>
>
Free Online Photosharing - Share your photos online with your friends and
family!
Visit http://www.inbox.com/photosharing to find out more!
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