Re: [R] Efficient way to convert covariance to Euclidian distance matrix
Rolf Turner r.turner at auckland.ac.nz writes: On 10/31/13 23:14, Takatsugu Kobayashi wrote: I am struggling to come up with an efficient vectorized way to convert 20Kx20K covariance matrix to a Euclidian distance matrix as a surrogate for dissimilarity matrix. Hopefully I can apply multidimensional scaling for mapping these 20K points (commercial products). My suspicion is that with a 20K x 20K covariance matrix: * nothing will work * even if it did, the results would be meaningless numerical noise. I.e. Get real. FWIW, I have tried NMDS for 19.2 K observations. It worked. The results looked sensible (i.e., they were not meaningless numerical noise). It was not fast, though, but it can be done. Cheers, Jari Oksanen PS. Sorry for excessive pruning, but gmane does not allow me post if I don't remove some quoted lines. __ 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] ascii-grid export
hi, I want to export in ascii-grid file a semivariogram map that I have did with gstat library. How can I make it? Somebody can help me? thanks! enzo -- Enzo Cocca (PhD Candidate) Research Fellow Università di Napoli L'Orientale mail: enzo@gmail.com cell: +393495087014 [[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] mapping data to a geographic map of Europe
Dear Claudia, I have written a tutorial for this task here; http://www.markuskainu.fi/r-tutorial/eurostat/spatial.html It uses the shapefile provided by Gisco and plots data from Eurostat. Packages rgdal and maptools are used to process the data and SpatialPolygonDataFrame is fortified into data.frame and plotted using ggplot2-package. Smaterpoland-package is used to access Eurostat data. Best, Markus Kainu 2013/11/1 palad...@trustindata.de Hi Jean, nevertheless this page R-bloggers looks realy interesting so I'll work through the tutorial. Thanks again for recommanding this web-site. Best regards Claudia Zitat von Adams, Jean jvad...@usgs.gov: Claudia, I have not worked through the example myself. Since you seem to be getting errors, perhaps a different example would help. Here are some more choropleth maps (although these use US states rather than European countries). http://blog.**revolutionanalytics.com/2009/**11/choropleth-challenge-** result.htmlhttp://blog.revolutionanalytics.com/2009/11/choropleth-challenge-result.html Jean On Fri, Nov 1, 2013 at 12:04 PM, palad...@trustindata.de wrote: Hi Jean, thanks again for your response. As I told you I did the downloads and double checked if I selected the right directory. But I noticed right now what happend: The command in the example is : eurMap - readShapePoly(fn=NUTS_2010_60M_SH/Shape/data/NUTS_RG_60M_ 2010) But it should be : eurMap - readShapePoly(fn=NUTS_2010_60M_SH/data/ggg/NUTS_RG_60M_** 2010) Because if you do the downloads and unzip these data there is no such think as a Shape directory. Now eurMap - readShapePoly(fn=NUTS_2010_ 60M_SH/data/NUTS_RG_60M_2010) works. What happens now is that after typing: eurEduMapDf - merge(eurMapDf, eurEdu, by.x=id, by.y=GEO) I get another error message because eurMapDf is unknown. So I supposed it should be: eurEduMapDf - merge(eurMap, eurEdu, by.x=id, by.y=GEO) But this doesn't work either.The error message this time is: undefined column selected. Did I do something wrong? Best regards Claudia Zitat von Adams, Jean jvad...@usgs.gov: Claudia, You should cc r-help on all correspondence so that others can follow the thread. In the second paragraph of the link I sent you http://www.r-bloggers.com/maps-in-r-choropleth-maps/http://www.r-bloggers.com/**maps-in-r-choropleth-maps/ htt**p://www.r-bloggers.com/maps-**in-r-choropleth-maps/http://www.r-bloggers.com/maps-in-r-choropleth-maps/ a link is provided for the NUTS data, The polygons for drawing the administrative boundaries were obtained from this link. In particular, the NUTS 2010 shapefile in the 1:60 million scale was downloaded and used. The other available scales would allow the drawing of better defined maps, but at a computational cost. The zipped file has to be extracted in a folder of choice for using it later. http://epp.eurostat.ec.europa.eu/portal/page/portal/gisco_ Geographical_information_maps/popups/references/ administrative_units_ **statistical_units_1http://**epp.eurostat.ec.europa.eu/** portal/page/portal/gisco_**Geographical_information_maps/** popups/references/**administrative_units_**statistical_units_1http://epp.eurostat.ec.europa.eu/portal/page/portal/gisco_Geographical_information_maps/popups/references/administrative_units_statistical_units_1 If you want to follow the example, you will need to download this data to your computer and then make sure that you refer to the appropriate directory when using the readShapePoly() function. Jean On Wed, Oct 30, 2013 at 11:14 AM, palad...@trustindata.de wrote: Hi Jean, thank you for your advice. The page looks quite interesting and I tried the example in GNU R. I did all the downloads. But Just in the beginnig after typing eurMap - readShapePoly(fn=NUTS_2010_**60M_SH/Shape/data/NUTS_RG_ **60M_ 2010) I get the following error message: Error in getinfo.shape(filen) : Error opening SHP file To you have an idea what I did wrong? Thanks a lot and best regards Claudia Zitat von Adams, Jean jvad...@usgs.gov: Check out this link for some examples http://www.r-bloggers.com/**maps-in-r-choropleth-maps/http://www.r-bloggers.com/maps-in-r-choropleth-maps/ htt**p://www.r-bloggers.com/**maps-**in-r-choropleth-maps/http://www.r-bloggers.com/**maps-in-r-choropleth-maps/ htt**p://www.r-bloggers.com/**maps-**in-r-choropleth-maps/http://www.r-bloggers.com/maps-**in-r-choropleth-maps/ h**ttp://www.r-bloggers.com/maps-**in-r-choropleth-maps/http://www.r-bloggers.com/maps-in-r-choropleth-maps/ Jean On Tue, Oct 29, 2013 at 12:02 PM, palad...@trustindata.de wrote: Hello, I would like to draw a map of Europe. Each country should be colored depending on how it scores in an index called GPIndex. Say a dark red for real bad countries a light red for those which are
Re: [R] ascii-grid export
If I understand what you are up to, my pander package might help. You mean something like this? I used the example form the package manual. library(pander) data(meuse) coordinates(meuse) = ~x+y pander(variogram(log(zinc)~1, meuse)) np dist gamma dir.hor dir.ver id -- --- - - 57 79.29 0.1234 0 0 var1 299 164 0.2162 0 0 var1 419 267.4 0.3028 0 0 var1 457 372.7 0.4121 0 0 var1 547 478.5 0.4634 0 0 var1 533 585.3 0.5647 0 0 var1 574 693.1 0.569 0 0 var1 564 796.2 0.6187 0 0 var1 589 903.1 0.6471 0 0 var1 543 1011 0.6916 0 0 var1 500 1118 0.7034 0 0 var1 477 1221 0.6039 0 0 var1 452 1329 0.6517 0 0 var1 457 1437 0.5665 0 0 var1 415 1543 0.5748 0 0 var1 Best, Gergely On 2 November 2013 09:55, Enzo Cocca enzo@gmail.com wrote: hi, I want to export in ascii-grid file a semivariogram map that I have did with gstat library. How can I make it? Somebody can help me? thanks! enzo -- Enzo Cocca (PhD Candidate) Research Fellow Università di Napoli L'Orientale mail: enzo@gmail.com cell: +393495087014 [[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. [[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] R Packages in Mac
Hello everyone, I am interested in finding out why some packages don't work on Mac like the package 'vcd' Is there a fix? -- Thanks, Jim. [[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] Path Analysis
Hello, I have just started to work on a path analysis (see attached image for the diagram), but I have encountered an error message. This is the code I have used: cov_matrix-var(xdata) library(sem) model.xdata-specifyModel() x1 - y2, xy12, NA x2 - y1, xy21, NA y1 - y2, yy12, NA y2 - y3, yy23, NA y2 - y4, yy24, NA y3 - y4, yy34, NA y2 - y2, y2error, NA y1 - y1, y1error, NA y3 - y3, y3error, NA y4 - y4, y4error, NA model.xdata.sem - sem(model.xdata, cov_matrix, nrow(xdata)) and the error message is: Error in csem(model = model.description, start, opt.flag = 1, typsize = typsize, : The matrix is non-invertable. I fear to have a problem in the data. I would be very grateful if you could help me to solve this problem and proceed with my analyses. thank you in advance for your help! Sarah [[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] how to compute correlation between times (with buffer before and after times)?
Dear forum members: I have two series of times to correlate. Additionally, I have to allow for a buffer before and after the times so that they can be within 20 seconds of each other and not seem discordant. Example of my data: Time 1 Time 2 9:26 9:26 10:31 10:29 9:22 9:35 9:35 9:38 9:37 9:28 9:28 9:17 9:16 9:34 9:34 9:08 9:07 Thanks, Julia [[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] R Packages in Mac
On 02/11/2013 17:03, Jim Silverton wrote: Hello everyone, I am interested in finding out why some packages don't work on Mac like the package 'vcd' Is there a fix? What does don't work mean? That one does: see http://cran.r-project.org/web/packages/vcd/index.html and the results page. Vague false accusations are unfair to the package maintainers and CRAN team. You were asked not to send HTML mail and to ask on the correct list: see the posting guide. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ 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] R Packages in Mac
The vcd package works for me on a mac. Please be more specific, describe what you did, and what happened that you found surprising. Also include the output of sessionInfo() Best, Ista On Sat, Nov 2, 2013 at 1:03 PM, Jim Silverton jim.silver...@gmail.com wrote: Hello everyone, I am interested in finding out why some packages don't work on Mac like the package 'vcd' Is there a fix? -- Thanks, Jim. [[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.
Re: [R] Path Analysis
Dear Sarah, It's generally a good idea to include a reproducible example if you want to get help with a problem, but in this case it's a safe bet that the problem is that the model you specified has no variance or covariance parameters for the variables x1 and x2, which, I assume, you mean to be exogenous. The easiest way to include these variances and covariance in the model is to specify the argument fixed.x=c(x1, x2) in the call to sem(). In addition: (1) Your model is fully recursive (guessing that all the x's and y's are observed variables), and so it amounts to four OLS regressions. You could just use lm() to fit the model. (2) It's generally easier in the sem package to use specifyEquations() than specifyModel() for model specification. (3) If you have the original data set, as you do, it's generally preferable to use the data argument to sem() than to pass it the covariance matrix for the observed variables. I hope that this helps, John John Fox McMaster University Hamilton, Ontario, Canada http://socserv.mcmaster.ca/jfox/ On Sat, 2 Nov 2013 11:02:31 +0100 Sarah Rogers rogerssara...@gmail.com wrote: Hello, I have just started to work on a path analysis (see attached image for the diagram), but I have encountered an error message. This is the code I have used: cov_matrix-var(xdata) library(sem) model.xdata-specifyModel() x1 - y2, xy12, NA x2 - y1, xy21, NA y1 - y2, yy12, NA y2 - y3, yy23, NA y2 - y4, yy24, NA y3 - y4, yy34, NA y2 - y2, y2error, NA y1 - y1, y1error, NA y3 - y3, y3error, NA y4 - y4, y4error, NA model.xdata.sem - sem(model.xdata, cov_matrix, nrow(xdata)) and the error message is: Error in csem(model = model.description, start, opt.flag = 1, typsize = typsize, : The matrix is non-invertable. I fear to have a problem in the data. I would be very grateful if you could help me to solve this problem and proceed with my analyses. thank you in advance for your help! Sarah [[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.
[R] How to obtain nonparametric baseline hazard estimates in the gamma frailty model?
I can easily get the other parameter estimates by using coxph() but don't know how to get the baseline hazard estimates from it. Does anyone know how to obtain nonparametric baseline hazard estimates in the gamma frailty model? Thanks, YH [[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] (gam) formula: Why different results for terms being factor vs. numeric?
Dear Bert, Thanks for helping. Your questions 'answers' why I get the expected behavior if 'group' is a factor. My question was why I don't get the expected behavior if 'group' is not a factor. From a theoretical (non-programming) point of view, there is no difference in a factor with two levels and a 0-1 (bool/integer) variable (in my case the 1-2 variable 'group'). gam() interprets these inputs differently, thus distinguishes these cases (and I was wondering why; In my opinion, this is a purely R/mgcv related question and belongs here). As it turned out, the problem was merely the following: By using factors and thus specifying a GAM, the intercept was 'hidden' in the estimated coefficients. When using integers as group variables, this is a glm and there one needs the intercept. The examples below provide the details. With best wishes, Marius require(mgcv) n - 10 yrs - 2000+seq_len(n) loss - c(seq_len(n)+runif(n), 5+seq_len(n)+runif(n)) ## Version 1: gam() with 'group' as factor # set.seed(271) dat - data.frame(year = rep(yrs, 2), group = as.factor(rep(1:2, each=n)), # could also be A, B resp = loss) fit1 - glm(resp ~ year + group - 1, data=dat) plot(yrs, fit1$fitted.values[seq_len(n)], type=l, ylim=range(dat$resp), xlab=Year, ylab=Response) # fit group A; mean over all responses in this group lines (yrs, fit1$fitted.values[n+seq_len(n)], col=blue) # fit group B; mean over all responses in this group points(yrs, dat$resp[seq_len(n)]) # actual response group A points(yrs, dat$resp[n+seq_len(n)], col=blue) # actual response group B ## Version 2: gam() with 'group' as numeric (= glm) ### set.seed(271) dat - data.frame(year = rep(yrs, 2), group = rep(1:2, each=n), # could also be 0:1 resp = loss) fit2 - glm(resp ~ year + group - 1, data=dat) # (*) plot(yrs, fit2$fitted.values[seq_len(n)], type=l, ylim=range(dat$resp), xlab=Year, ylab=Response) # fit group A; mean over all responses in this group lines (yrs, fit2$fitted.values[n+seq_len(n)], col=blue) # fit group B; mean over all responses in this group points(yrs, dat$resp[seq_len(n)]) # actual response group A points(yrs, dat$resp[n+seq_len(n)], col=blue) # actual response group B ## Note: without '-1' (intercept) in (*), an unexpected behavior results ## Explanation: ## S. Wiki GAM (without beta_0): ##g(E(Y)) = f_1(x_1) + f_2(x_2) ## where f_i(x_i) may be functions with a specified parametric form (for example a ## polynomial, or a coefficient depending on the levels of a factor variable) ## = for f_i's being coefficients (numbers) beta_i, this is a GLM: ##g(E(Y)) = beta_1 x_1 + beta_2 x_2 (x_1 = year, x_2 = group) ## Problem: (*) does not specify an intercept and thus the lines are not picked up correctly fit2$coefficients ## Version 3: Version 2 with intercept # set.seed(271) dat - data.frame(year = rep(yrs, 2), group = rep(1:2, each=n), # could also be 0:1 resp = loss) fit3 - glm(resp ~ year + group, data=dat) # now with intercept plot(yrs, fit3$fitted.values[seq_len(n)], type=l, ylim=range(dat$resp), xlab=Year, ylab=Response) # fit group A; mean over all responses in this group lines (yrs, fit3$fitted.values[n+seq_len(n)], col=blue) # fit group B; mean over all responses in this group points(yrs, dat$resp[seq_len(n)]) # actual response group A points(yrs, dat$resp[n+seq_len(n)], col=blue) # actual response group B ## = correct/as expected fit3$coefficients ## Note: in Version 1, the intercept is already included in the group coefficients: fit1$coefficients On Tue, Oct 29, 2013 at 9:31 PM, Bert Gunter gunter.ber...@gene.com wrote: Think about it. How can one define a smooth term with a factor??? Further discussion is probably offtopic. Post on stats.stackexchange.com if it still isn't obvious. Cheers, Bert __ 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] ascii-grid export
Or do you mean you want to write the gridded output of an interpolation you did (perhaps using kriging) in gstat as an ESRI ASCII Grid file for reading into a GIS? If so, you can probably do it with writeGDAL from the rgdal package, or writeRaster from the raster package. I don't really know what a 'semivariogram map' is. On Sat, Nov 2, 2013 at 8:55 AM, Enzo Cocca enzo@gmail.com wrote: hi, I want to export in ascii-grid file a semivariogram map that I have did with gstat library. How can I make it? Somebody can help me? thanks! enzo -- Enzo Cocca (PhD Candidate) Research Fellow Università di Napoli L'Orientale mail: enzo@gmail.com cell: +393495087014 [[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] Installing RCurl: 'configure' exists but is not executable
That seems OK. Are you trying to install the RCurl package from source? IIRC, the configure script is commonly used in GNU-style, compile-from-source installations. -- Mike On Fri, Nov 1, 2013 at 8:38 PM, Rainer Schuermann rainer.schuerm...@gmx.net wrote: # ls -l `which curl-config` -rwxr-xr-x 1 root root 6327 Oct 20 15:25 /usr/bin/curl-config On Friday 01 November 2013 20:21:36 Michael Hannon wrote: The error message doesn't seem to refer to the tmp directory. What do you get from: ls -l `which curl-config` -- Mike On Fri, Nov 1, 2013 at 7:43 PM, Rainer Schuermann rainer.schuerm...@gmx.net wrote: I'm trying to install.packages( RCurl ) as root but get ERROR: 'configure' exists but is not executable I remember having had something like that before on another machine and tried in bash what is described here http://mazamascience.com/WorkingWithData/?p=1185 and helped me before: # mkdir ~/tmp # export TMPDIR=~/tmp and added, just in case, # chmod u+x $TMPDIR which apparently does what it should # ls -ld $TMPDIR drwxrwxrwx 2 root root 4096 Nov 1 08:59 /root/tmp but it doesn't help, I get the same error. What else can I try? Thanks in advance, Rainer sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_3.0.2 __ 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. [[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. [[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] Package(s) for making waffle plot-like figures?
On 11/02/2013 10:35 AM, Zhao Jin wrote:
Dear all,
I am trying to make a series of waffle plot-like figures for my data to
visualize the ratios of amino acid residues at each position. For each one
of 37 positions, there may be one to four different amino acid residues. So
the data consist of the positions, what residues are there, and the ratios
of residues. The ratios of residues at a position add up to 100, or close
to 100 (more on this soon)*. I am hoping to make a *square* waffle
plot-like figure for each position, and fill the 10 X 10 grids with colors
representing each amino acid residue and areas for grids of a certain color
corresponding to the ratio of that residue. Then I could line up all the
plots in one row from position 1 to position 37.
*: if the sum of the ratios is less than 100 at a position, that's because
of an unknown residue which I did not include in the table.
I am attaching the dput output for my data here:
structure(list(position = c(1L, 2L, 3L, 4L, 4L, 5L, 6L, 7L, 7L,
8L, 9L, 9L, 9L, 10L, 10L, 11L, 11L, 12L, 12L, 13L, 13L, 14L,
15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 22L, 23L, 24L, 25L, 26L,
26L, 27L, 28L, 29L, 29L, 30L, 31L, 32L, 33L, 34L, 34L, 35L, 35L,
36L, 36L, 36L, 37L, 37L), residue = structure(c(9L, 4L, 18L,
7L, 9L, 7L, 12L, 3L, 4L, 1L, 7L, 9L, 12L, 1L, 4L, 4L, 13L, 5L,
14L, 2L, 18L, 3L, 16L, 9L, 17L, 15L, 7L, 5L, 5L, 7L, 17L, 13L,
15L, 11L, 6L, 13L, 16L, 14L, 10L, 13L, 17L, 1L, 1L, 17L, 1L,
12L, 1L, 5L, 3L, 6L, 8L, 7L, 9L), .Label = c(A, C, D, E,
G, H, I, K, L, M, N, P, Q, R, S, T, V,
Y), class = factor), ratio = c(99L, 100L, 100L, 1L, 99L,
100L, 100L, 1L, 98L, 100L, 10L, 87L, 3L, 79L, 9L, 12L, 84L, 99L,
1L, 83L, 13L, 100L, 100L, 100L, 100L, 99L, 100L, 100L, 100L,
98L, 2L, 100L, 100L, 100L, 2L, 98L, 100L, 100L, 1L, 99L, 100L,
100L, 98L, 100L, 95L, 5L, 98L, 2L, 3L, 95L, 1L, 1L, 98L)), .Names =
c(position,
residue, ratio), class = data.frame, row.names = c(1,
2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15,
17, 18, 19, 20, 23, 25, 27, 28, 29, 30, 31,
32, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44,
45, 46, 47, 48, 50, 51, 52, 53, 54, 56, 57,
58, 59, 60, 61, 62, 63, 64, 65))
Inspired by a statexchange post, I am using these scripts to make the plots
:
library(ggplot2)
col4=c('#E66101','#FDB863','#B2ABD2','#5E3C99')
dflist=list()
for (i in 1:37){
residue_num=length(which(df$position==i))
dflist[[i]]=df[df$position==i,2:3]
waffle=expand.grid(y=1:residue_num,x=seq_len(ceiling(sum(dflist[[i]]$ratio)/residue_num)))
residuevec=rep(dflist[[i]]$residue,dflist[[i]]$ratio)
waffle$residue=c(as.vector(residuevec),rep(NA,nrow(waffle)-length(residuevec)))
png(paste('plot',i,'.png',sep=''))
print(ggplot(waffle, aes(x = x, y = y, fill = residue)) + geom_tile(color =
white) + scale_fill_manual(residue,values = col4) + coord_equal() +
theme(panel.grid.minor=element_blank(),panel.grid.major=element_blank())
+ theme(axis.ticks=element_blank()) +
theme(axis.text.x=element_blank(),axis.text.y=element_blank()) +
theme(axis.title.x=element_blank(),axis.title.y=element_blank())
)
dev.off()}
With my scripts, I could make a waffle plot, but not a *square* 10 X 10
waffle plot. Also, the grid size differs for positions with different
numbers of residues. I am suspecting that I didn't use coord_equal()
correctly.
So I wonder how I can make the plots like I described above in ggplot2 or
with some other packages. Also, is there a way to assign a color to
different residues, say, purple for alanine, blue for glycine, etc, and
incorporate that information in the for loop?
Hi Zhao,
By beginning with a 10x10 matrix of NA values and then replacing some of
them with a color, I think you can do what you want. First you need a
function to fill one corner of your matrix with values, leaving the rest
uncolored (i.e. NA):
fill.corner-function(x,nrow,ncol) {
xlen-length(x)
if(nrow*ncol xlen) {
newmat-matrix(NA,nrow=nrow,ncol=ncol)
xside-1
while(xside*xside xlen) xside-xside+1
row=1
col=1
for(xindex in 1:xlen) {
newmat[row,col]-x[xindex]
if(row == xside) {
col-col+1
row-1
}
else row-row+1
}
return(newmat)
}
cat(Too many values in x for,xrow,by,xcol,\n)
}
Then you have to massage your data frame into 37 smaller data frames,
create matrices with the values and colors to display on your 37 waffle
plots:
library(plotrix)
# get an alphabet of colors
alphacol-rainbow(18)
# the actual values in the plotted matrix don't matter
fakemat-matrix(1:100,nrow=10)
# pick off the positions one by one
for(pos in 1:37) {
posdf-zjdat[zjdat$position == pos,]
for(res in 1:dim(posdf)[1]) {
if(res == 1)
rescol-rep(alphacol[as.numeric(posdf$residue[res])],
posdf$ratio[res])
else
rescol-c(rescol,rep(alphacol[as.numeric(posdf$residue[res])],
posdf$ratio[res]))
}
if(!is.null(resmat-fill.corner(rescol,10,10)))
color2D.matplot(fakemat,border=lightgray,cellcolors=resmat,
yrev=FALSE,main=c(pos,length(resmat)))
}
That might get you started. In fact, I might even write a waffle
Re: [R] plot time series data in wide format
On 11/02/2013 11:08 AM, Gary Dong wrote: Dear R users, I wonder if there is a way that I can plot a time series data which is in a wide format like this: CITY_NAME 2000Q12000Q2 2000Q32000Q4 2001Q1 2001Q2 2001Q3 2001Q4 2002Q1 2002Q2 CITY1100.5210 101.9667 103.24933 104.0506 104.4317 105.3921 106.7643 107.5202 107.2561 107.8184 CITY2100.0412 100.6146 103.20293 104.0867 104.6612 106.6126 109.3514 110.1943 110.9480 113.0071 CITY3 99.589599.2298 99.2694799.4101 100.5776 101.3719 101.5957 102.2411 103.4390 105.1745 CITY4 99.6491 101.5386 104.90953 106.1065 108.1785 110.6845 113.3746 114.1254 116.2121 119.1033 CITY5100.9828 103.6847 105.04793 106.5925 108.7437 110.5549 111.9343 112.6704 113.6201 115.3020 Ideally, each city of the five city is represented by a line in the plot. Hi Gary, I'm not sure that this is exactly what you want, but: library(plotrix) # use window() if you are using Windows x11(width=10,height=5) bumpchart(garydf[,2:11],rank=FALSE,labels=garydf[,1]) Jim __ 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.
