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: jrkrid...@inbox.com Subject: RE: [R] smoothScatter plot To: zhyjiang2...@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: zhyjiang2...@hotmail.com Sent: Mon, 8 Oct 2012 22:46:35 +0800 To: jrkrid...@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: jrkrid...@inbox.com > Subject: RE: [R] smoothScatter plot > To: zhyjiang2...@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: zhyjiang2...@hotmail.com > Sent: Sat, 6 Oct 2012 01:01:41 +0800 > To: jrkrid...@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: jrkrid...@inbox.com > Subject: RE: [R] smoothScatter plot > To: zhyjiang2...@hotmail.com > CC: r-help@r-project.org > > In line > > John Kane > Kingston ON Canada > > -----Original Message----- > From: zhyjiang2...@hotmail.com > Sent: Fri, 5 Oct 2012 05:41:29 +0800 > To: jrkrid...@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: jrkrid...@inbox.com > Subject: RE: [R] smoothScatter plot > To: zhyjiang2...@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: zhyjiang2...@hotmail.com > Sent: Thu, 4 Oct 2012 05:19:14 +0800 > To: jrkrid...@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: jrkrid...@inbox.com > > Subject: RE: [R] smoothScatter plot > > To: zhyjiang2...@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: zhyjiang2...@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! 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