Re: [R] smoothScatter plot
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
Re: [R] smoothScatter plot
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
Re: [R] smoothScatter plot
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-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: 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
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
Re: [R] smoothScatter plot
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
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 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
[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 attachment: sm1.pngattachment: s1.png__ 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.
Re: [R] smoothScatter plot
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! __ 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.
[R] SmoothScatter plot range issue
Hello, I am attempting to use smoothScatter to plot a heatmap of locations of events in an x-y axis. When I plot the heatmap without passing xlim and ylim parameters, it fills the plot area but the perspective is a bit skewed. I would like to standardize these plots to a uniform window size that does not depend on the range of values in the dataframe. However, when I resize the plot using xlim or ylim, there is a light blue background that surrounds the immediate area of the data (correspnding to the range of the points listed in the dataframe), surrounded by extra white space for the new xlim and ylim values I have added. Some of the rings around the datapoints are also cut off at the margins. I would like to stop the plot from being cut off, and want this light blue range to extend throughout the entire area of the resized plot. I have attempted to add NAs, but it has no effect on expanding this light blue plot area. Code is below. xyz is a dataframe containing two columns with corresponding x and y values library(geneplotter) library(RColorBrewer) layout(matrix(1:1, ncol=2, byrow=TRUE)) smoothScatter(xyz, nrpoints=0, xlim=c(-3,3), ylim=c(0,5),colramp=colorRampPalette(c(#f8f8ff, white, #736AFF, cyan, yellow, #F87431, #FF7F00, red, #7E2217))) ###END Thanks very much for any help, Jason [[alternative HTML version deleted]] __ 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.
Re: [R] SmoothScatter plot range issue
Hi, Bioconductor.org is the home of the geneplotter package. You get a quicker response if you ask there. /Henrik On Mon, Sep 22, 2008 at 7:06 AM, Jason Pare [EMAIL PROTECTED] wrote: Hello, I am attempting to use smoothScatter to plot a heatmap of locations of events in an x-y axis. When I plot the heatmap without passing xlim and ylim parameters, it fills the plot area but the perspective is a bit skewed. I would like to standardize these plots to a uniform window size that does not depend on the range of values in the dataframe. However, when I resize the plot using xlim or ylim, there is a light blue background that surrounds the immediate area of the data (correspnding to the range of the points listed in the dataframe), surrounded by extra white space for the new xlim and ylim values I have added. Some of the rings around the datapoints are also cut off at the margins. I would like to stop the plot from being cut off, and want this light blue range to extend throughout the entire area of the resized plot. I have attempted to add NAs, but it has no effect on expanding this light blue plot area. Code is below. xyz is a dataframe containing two columns with corresponding x and y values library(geneplotter) library(RColorBrewer) layout(matrix(1:1, ncol=2, byrow=TRUE)) smoothScatter(xyz, nrpoints=0, xlim=c(-3,3), ylim=c(0,5),colramp=colorRampPalette(c(#f8f8ff, white, #736AFF, cyan, yellow, #F87431, #FF7F00, red, #7E2217))) ###END Thanks very much for any help, Jason [[alternative HTML version deleted]] __ 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. __ 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.
