Re: [R] how to add 3d-points to bplot {rms} figure?
On Apr 12, 2012, at 6:09 PM, phi771 wrote: h! thank you a lot for your effort and help. i preferred a 3d view of the surface in order to see how well it fits the real data (from the file). i will play around with the functions you have mentioned and post my results or further problems. this will probably take a few days :( can anybody answer if i can extract the mesh in x,y,z coordinates from the bplot? With the example you offered (but failed to include as context): You need to learn to use str() str(bpl) # output too long str(bpl$panel.args.common] ) # output still too long str(bpl$panel.args.common[c(x,y,z)] ) List of 3 $ x: num [1:4] -2.44 -2.44 -2.43 -2.42 -2.41 ... $ y: num [1:4] -0.196 -0.196 -0.196 -0.196 -0.196 ... $ z: num [1:4] 107 106 106 105 104 ... -- David Winsemius, MD West Hartford, CT __ 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] how to add 3d-points to bplot {rms} figure?
h! thank you a lot for your effort and help. i preferred a 3d view of the surface in order to see how well it fits the real data (from the file). i will play around with the functions you have mentioned and post my results or further problems. this will probably take a few days :( can anybody answer if i can extract the mesh in x,y,z coordinates from the bplot? thank you again. -- View this message in context: http://r.789695.n4.nabble.com/how-to-add-3d-points-to-bplot-rms-figure-tp4544050p4553227.html Sent from the R help mailing list archive at Nabble.com. __ 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] how to add 3d-points to bplot {rms} figure?
Hello! I have created a bplot-figure using this code: *file - 2dcali_red.ttt ux-as.matrix(read.table(file, dec = ,)) mode(ux)-'numeric' vel-ux[,1] ang-ux[,2] x-ux[,3] y-ux[,4] dat- data.frame(ang=ang, x=x,y=y) require(rms) ddist2 - datadist(dat) options(datadist=ddist2) fitn - lrm(ang ~ rcs(x,4) + rcs(y,4), data=dat) predi - Predict(fitn, x, y) bplot(predi,lfun=wireframe, screen = list(z = -40, x = -80), drape=TRUE)* The file 2dcali_red.ttt consists of 4 columns can be found here : http://www.color-space.de/upload/dl/2dcali_red.ttt link The code gives me the bplot-figure, which looks like this: http://r.789695.n4.nabble.com/file/n4544050/Screen_shot_2012-04-10_at_12.04.24_AM.png Now I want to add some 3d data (x,y,z) to this plot (like scatterplot3d), but i don't know how. I also don't know how to extract the x,y,z mesh as coordinates from the bplot. Some help would be very appreciated. Thank you! -- View this message in context: http://r.789695.n4.nabble.com/how-to-add-3d-points-to-bplot-rms-figure-tp4544050p4544050.html Sent from the R help mailing list archive at Nabble.com. __ 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] how to add 3d-points to bplot {rms} figure?
On Apr 9, 2012, at 6:24 PM, phi771 wrote: Hello! I have created a bplot-figure using this code: *file - 2dcali_red.ttt ux-as.matrix(read.table(file, dec = ,)) mode(ux)-'numeric' vel-ux[,1] ang-ux[,2] x-ux[,3] y-ux[,4] dat- data.frame(ang=ang, x=x,y=y) require(rms) ddist2 - datadist(dat) options(datadist=ddist2) fitn - lrm(ang ~ rcs(x,4) + rcs(y,4), data=dat) predi - Predict(fitn, x, y) bplot(predi,lfun=wireframe, screen = list(z = -40, x = -80), drape=TRUE)* The file 2dcali_red.ttt consists of 4 columns can be found here : http://www.color-space.de/upload/dl/2dcali_red.ttt link The code gives me the bplot-figure, which looks like this: http://r.789695.n4.nabble.com/file/n4544050/Screen_shot_2012-04-10_at_12.04.24_AM.png Now I want to add some 3d data (x,y,z) to this plot (like scatterplot3d), but i don't know how. I also don't know how to extract the x,y,z mesh as coordinates from the bplot. Some help would be very appreciated. Thank you! That is most probably a lattice::wireframe object. You could use 'trellis.focus' or the 'layer' functions in pkg::latticeExtra to attempt panel.3dbars() additions. I haven't actually done this, but I have added panel function results to the lattice::contourplots that are created byrms/Hmisc. The 3d aspect adds a significant level of extra work: http://tolstoy.newcastle.edu.au/R/e2/help/06/10/3274.html Maybe a contourplot would suffice? -- David Winsemius, MD West Hartford, CT __ 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] how to add 3d-points to bplot {rms} figure?
On Apr 9, 2012, at 10:39 PM, David Winsemius wrote: On Apr 9, 2012, at 6:24 PM, phi771 wrote: Hello! I have created a bplot-figure using this code: *file - 2dcali_red.ttt ux-as.matrix(read.table(file, dec = ,)) mode(ux)-'numeric' vel-ux[,1] ang-ux[,2] x-ux[,3] y-ux[,4] dat- data.frame(ang=ang, x=x,y=y) require(rms) ddist2 - datadist(dat) options(datadist=ddist2) fitn - lrm(ang ~ rcs(x,4) + rcs(y,4), data=dat) predi - Predict(fitn, x, y) bplot(predi,lfun=wireframe, screen = list(z = -40, x = -80), drape=TRUE)* The file 2dcali_red.ttt consists of 4 columns can be found here : http://www.color-space.de/upload/dl/2dcali_red.ttt link The code gives me the bplot-figure, which looks like this: http://r.789695.n4.nabble.com/file/n4544050/Screen_shot_2012-04-10_at_12.04.24_AM.png Now I want to add some 3d data (x,y,z) to this plot (like scatterplot3d), but i don't know how. I also don't know how to extract the x,y,z mesh as coordinates from the bplot. Some help would be very appreciated. Thank you! That is most probably a lattice::wireframe object. You could use 'trellis.focus' or the 'layer' functions in pkg::latticeExtra to attempt panel.3dbars() additions. I haven't actually done this, but I have added panel function results to the lattice::contourplots that are created byrms/Hmisc. The 3d aspect adds a significant level of extra work: http://tolstoy.newcastle.edu.au/R/e2/help/06/10/3274.html There is also a panel.3d.identify and panel.identify.cloud that might be needed: https://r-forge.r-project.org/scm/viewvc.php/pkg/R/interaction.R?view=markuprevision=675root=lattice My efforts at adding bars to that plot have failed so far. This does not do anything useful: trellis.focus(panel, 1, 1) panel.3dbars(x=-1.5, y=-.1, z=0,distance=20, col=red, xlim=c(-2.4,-1), ylim=c(-0.15, 0.15), zlim=c(-50,100), xlim.scaled=c(-0.5,0.5), ylim.scaled=c(-0.5,0.5), zlim.scaled=c(-0.5,0.5), zero.scaled=25) trellis.unfocus() Maybe a contourplot would suffice? David Winsemius, MD West Hartford, CT __ 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] how to add 3d-points to bplot {rms} figure?
Below. -- Bert On Mon, Apr 9, 2012 at 7:39 PM, David Winsemius dwinsem...@comcast.net wrote: On Apr 9, 2012, at 6:24 PM, phi771 wrote: Hello! I have created a bplot-figure using this code: *file - 2dcali_red.ttt ux-as.matrix(read.table(file, dec = ,)) mode(ux)-'numeric' vel-ux[,1] ang-ux[,2] x-ux[,3] y-ux[,4] dat- data.frame(ang=ang, x=x,y=y) require(rms) ddist2 - datadist(dat) options(datadist=ddist2) fitn - lrm(ang ~ rcs(x,4) + rcs(y,4), data=dat) predi - Predict(fitn, x, y) bplot(predi,lfun=wireframe, screen = list(z = -40, x = -80), drape=TRUE)* The file 2dcali_red.ttt consists of 4 columns can be found here : http://www.color-space.de/upload/dl/2dcali_red.ttt link The code gives me the bplot-figure, which looks like this: http://r.789695.n4.nabble.com/file/n4544050/Screen_shot_2012-04-10_at_12.04.24_AM.png Now I want to add some 3d data (x,y,z) to this plot (like scatterplot3d), but i don't know how. I also don't know how to extract the x,y,z mesh as coordinates from the bplot. Some help would be very appreciated. Thank you! That is most probably a lattice::wireframe object. You could use 'trellis.focus' or the 'layer' functions in pkg::latticeExtra to attempt panel.3dbars() additions. I haven't actually done this, but I have added panel function results to the lattice::contourplots that are created byrms/Hmisc. The 3d aspect adds a significant level of extra work: And is generally a bad idea. Perspective plots of all types are much over-hyped. They are pretty, but the very act of creating artificial perspective for non-realistic shapes can distort perception and lead to misinterpretation of data. Parts of the scene hide other parts; it is difficult to quantitatively judge depths of valleys and heights of hills; etc. And, as David notes, it is very difficult to get right. http://tolstoy.newcastle.edu.au/R/e2/help/06/10/3274.html Maybe a contourplot would suffice? -- and is generally a much better, albeit less sexy, idea. -- David Winsemius, MD West Hartford, CT __ 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. -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm __ 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.
