
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.
> > 
> > ____________________________________________________________
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