David Winsemius

2017-Oct-09 16:32 UTC

### [R] example of geom_contour() with function argument

> On Oct 9, 2017, at 6:03 AM, Big Floppy Dog <bigfloppydog at gmail.com> wrote: > > Hello Ulrik, > > I apologize, but I can not see how to provide a pdf in place of the density > function which calculates a KDE (that is, something from the dataset in the > example). Can you please point to the specific example that might help? > > Here is what I get: > > require(mvtnorm) > require(ggplot2) > set.seed(1234) > xx <- data.frame(rmvt(100, df = c(13, 13))) > > > v <- ggplot(faithfuld, aes(waiting, eruptions, z = drmvt, df = c(13,13))) > v + geom_contour() > > Don't know how to automatically pick scale for object of type function. > Defaulting to continuous. > Error: Aesthetics must be either length 1 or the same as the data (5625): > x, y, z, df >That's not what I get:> v <- ggplot(faithfuld, aes(waiting, eruptions, z = drmvt, df = c(13,13))) > v + geom_contour()Error in FUN(X[[i]], ...) : object 'drmvt' not found> > ? faithfuld > str(faithfuld)Classes ?tbl_df?, ?tbl? and 'data.frame': 5625 obs. of 3 variables: $ eruptions: num 1.6 1.65 1.69 1.74 1.79 ... $ waiting : num 43 43 43 43 43 43 43 43 43 43 ... $ density : num 0.00322 0.00384 0.00444 0.00498 0.00542 ... So you are apparently trying to throw together code and data that you don't understand. The data you are using is already a density estimate designed to simply be plotted. It is not the original data. Furthermore you are passing drmvt that is apparently not in either the mvtnorm nor the ggplot2 packages. You should determine where that function is and then determine how to do a 2d estimate on the original data. I'm guessing this is homework so not inclined to offer a complete solution. -- David.> > Can you please tell me how to use this here? Or is some other example more > appropriate? > > TIA, > BFD > > > > On Mon, Oct 9, 2017 at 2:22 AM, Ulrik Stervbo <ulrik.stervbo at gmail.com> > wrote: > >> Hi BFD, >> >> ?geom_contour() *does* have helpful examples. Your Google-foo is weak: >> Searching for geom_contour brought me: http://ggplot2.tidyverse. >> org/reference/geom_contour.html as the first result. >> >> HTH >> Ulrik >> >> On Mon, 9 Oct 2017 at 08:04 Big Floppy Dog <bigfloppydog at gmail.com> wrote: >> >>> Can someone please point me to an example with geom_contour() that uses a >>> function? The help does not have an example of a function, and also I did >>> not find anything from online searches. >>> >>> TIA, >>> BFD >>> >>> >>> ------------------------------------------------------------ >>> ----------------------------------- >>> >>> How about geom_contour()? >>> >>> Am So., 8. Okt. 2017, 20:52 schrieb Ranjan Maitra <maitra at email.com>: >>> >>>> Hi, >>>> >>>> I am no expert on ggplot2 and I do not know the answer to your >>> question. I >>>> looked around a bit but could not find an answer right away. But one >>>> possibility could be, if a direct approach is not possible, to draw >>>> ellipses corresponding to the confidence regions of the multivariate t >>>> density and use geom_polygon to draw this successively? >>>> >>>> I will wait for a couple of days to see if there is a better answer >>> posted >>>> and then write some code, unless you get to it first. >>>> >>>> Thanks, >>>> Ranjan >>>> >>>> >>>> On Sun, 8 Oct 2017 09:30:30 -0500 Big Floppy Dog < >>> bigfloppydog at gmail.com> >>>> wrote: >>>> >>>>> Note: I have posted this on SO also but while the question has been >>>>> upvoted, there has been no answer yet. >>>>> >>>>> >>>> >>> https://stackoverflow.com/questions/46622243/ggplot- >>> plot-2d-probability-density-function-on-top-of-points-on-ggplot >>>>> >>>>> Apologies for those who have seen it there also but I thought that >>> this >>>>> list of experts may have someone who knows the answer. >>>>> >>>>> I have the following example code: >>>>> >>>>> >>>>> >>>>> require(mvtnorm) >>>>> require(ggplot2) >>>>> set.seed(1234) >>>>> xx <- data.frame(rmvt(100, df = c(13, 13))) >>>>> ggplot(data = xx, aes(x = X1, y= X2)) + geom_point() + >>> geom_density2d() >>>>> >>>>> >>>>> >>>>> It yields a scatterplot of X2 against X1 and a KDE contour plot of the >>>>> density (as it should). >>>>> >>>>> My question is: is it possible to change the contour plot to display >>>>> the contours >>>>> >>>>> of a two-dimensional density function (say dmvt), using ggplot2? >>>>> >>>>> The remaining figures in my document are in ggplot2 and therefore I >>>>> am looking for a ggplot2 solution. >>>>> >>>>> Thanks in advance! >>>>> >>>>> BFD >>>>> >>>>> [[alternative HTML version deleted]] >>>>> >>>>> ______________________________________________ >>>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >>>>> 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 at r-project.org mailing list -- To UNSUBSCRIBE and more, see >>> 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 at r-project.org mailing list -- To UNSUBSCRIBE and more, see > 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.David Winsemius Alameda, CA, USA 'Any technology distinguishable from magic is insufficiently advanced.' -Gehm's Corollary to Clarke's Third Law

Hi, This is not a HW problem, sadly: I was last in a classroom 30 years ago, and can no longer run off to the instructor :-( I apologize but I cut and paste the wrong snippet earlier and made a typo in doing so, but the result is the same with the more appropriate snippet. require(mvtnorm) require(ggplot2) set.seed(1234) xx <- data.frame(rmvt(100, df = c(13, 13))) v <- ggplot(data = xx, aes(x = X1, y = X2, z = dmvt, df = c(13,13))) v + geom_contour() Don't know how to automatically pick scale for object of type function. Defaulting to continuous. Error: Aesthetics must be either length 1 or the same as the data (100): x, y, z, df I do not understand how to put in a function as an argument to geom_contour() and the examples in the help fileor in the link that Ulrik sent are not very helpful to me. Hence, I was asking for some examples that might be helpful. I guess the answer is to make a second dataset that is regular and make the function estimate that, but how do I combine this? TIA. BFD On Mon, Oct 9, 2017 at 11:32 AM, David Winsemius <dwinsemius at comcast.net> wrote:> > > On Oct 9, 2017, at 6:03 AM, Big Floppy Dog <bigfloppydog at gmail.com> > wrote: > > > > Hello Ulrik, > > > > I apologize, but I can not see how to provide a pdf in place of the > density > > function which calculates a KDE (that is, something from the dataset in > the > > example). Can you please point to the specific example that might help? > > > > Here is what I get: > > > > require(mvtnorm) > > require(ggplot2) > > set.seed(1234) > > xx <- data.frame(rmvt(100, df = c(13, 13))) > > > > > > v <- ggplot(faithfuld, aes(waiting, eruptions, z = drmvt, df = c(13,13))) > > v + geom_contour() > > > > Don't know how to automatically pick scale for object of type function. > > Defaulting to continuous. > > Error: Aesthetics must be either length 1 or the same as the data (5625): > > x, y, z, df > > > > That's not what I get: > > > v <- ggplot(faithfuld, aes(waiting, eruptions, z = drmvt, df = c(13,13))) > > v + geom_contour() > Error in FUN(X[[i]], ...) : object 'drmvt' not found > > > > ? faithfuld > > str(faithfuld) > Classes ?tbl_df?, ?tbl? and 'data.frame': 5625 obs. of 3 variables: > $ eruptions: num 1.6 1.65 1.69 1.74 1.79 ... > $ waiting : num 43 43 43 43 43 43 43 43 43 43 ... > $ density : num 0.00322 0.00384 0.00444 0.00498 0.00542 ... > > So you are apparently trying to throw together code and data that you > don't understand. The data you are using is already a density estimate > designed to simply be plotted. It is not the original data. Furthermore you > are passing drmvt that is apparently not in either the mvtnorm nor the > ggplot2 packages. > > You should determine where that function is and then determine how to do a > 2d estimate on the original data. I'm guessing this is homework so not > inclined to offer a complete solution. > > -- > David. > > > > > > Can you please tell me how to use this here? Or is some other example > more > > appropriate? > > > > TIA, > > BFD > > > > > > > > On Mon, Oct 9, 2017 at 2:22 AM, Ulrik Stervbo <ulrik.stervbo at gmail.com> > > wrote: > > > >> Hi BFD, > >> > >> ?geom_contour() *does* have helpful examples. Your Google-foo is weak: > >> Searching for geom_contour brought me: http://ggplot2.tidyverse. > >> org/reference/geom_contour.html as the first result. > >> > >> HTH > >> Ulrik > >> > >> On Mon, 9 Oct 2017 at 08:04 Big Floppy Dog <bigfloppydog at gmail.com> > wrote: > >> > >>> Can someone please point me to an example with geom_contour() that > uses a > >>> function? The help does not have an example of a function, and also I > did > >>> not find anything from online searches. > >>> > >>> TIA, > >>> BFD > >>> > >>> > >>> ------------------------------------------------------------ > >>> ----------------------------------- > >>> > >>> How about geom_contour()? > >>> > >>> Am So., 8. Okt. 2017, 20:52 schrieb Ranjan Maitra <maitra at email.com>: > >>> > >>>> Hi, > >>>> > >>>> I am no expert on ggplot2 and I do not know the answer to your > >>> question. I > >>>> looked around a bit but could not find an answer right away. But one > >>>> possibility could be, if a direct approach is not possible, to draw > >>>> ellipses corresponding to the confidence regions of the multivariate t > >>>> density and use geom_polygon to draw this successively? > >>>> > >>>> I will wait for a couple of days to see if there is a better answer > >>> posted > >>>> and then write some code, unless you get to it first. > >>>> > >>>> Thanks, > >>>> Ranjan > >>>> > >>>> > >>>> On Sun, 8 Oct 2017 09:30:30 -0500 Big Floppy Dog < > >>> bigfloppydog at gmail.com> > >>>> wrote: > >>>> > >>>>> Note: I have posted this on SO also but while the question has been > >>>>> upvoted, there has been no answer yet. > >>>>> > >>>>> > >>>> > >>> https://stackoverflow.com/questions/46622243/ggplot- > >>> plot-2d-probability-density-function-on-top-of-points-on-ggplot > >>>>> > >>>>> Apologies for those who have seen it there also but I thought that > >>> this > >>>>> list of experts may have someone who knows the answer. > >>>>> > >>>>> I have the following example code: > >>>>> > >>>>> > >>>>> > >>>>> require(mvtnorm) > >>>>> require(ggplot2) > >>>>> set.seed(1234) > >>>>> xx <- data.frame(rmvt(100, df = c(13, 13))) > >>>>> ggplot(data = xx, aes(x = X1, y= X2)) + geom_point() + > >>> geom_density2d() > >>>>> > >>>>> > >>>>> > >>>>> It yields a scatterplot of X2 against X1 and a KDE contour plot of > the > >>>>> density (as it should). > >>>>> > >>>>> My question is: is it possible to change the contour plot to display > >>>>> the contours > >>>>> > >>>>> of a two-dimensional density function (say dmvt), using ggplot2? > >>>>> > >>>>> The remaining figures in my document are in ggplot2 and therefore I > >>>>> am looking for a ggplot2 solution. > >>>>> > >>>>> Thanks in advance! > >>>>> > >>>>> BFD > >>>>> > >>>>> [[alternative HTML version deleted]] > >>>>> > >>>>> ______________________________________________ > >>>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > >>>>> 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 at r-project.org mailing list -- To UNSUBSCRIBE and more, see > >>> 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 at r-project.org mailing list -- To UNSUBSCRIBE and more, see > > 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. > > David Winsemius > Alameda, CA, USA > > 'Any technology distinguishable from magic is insufficiently advanced.' > -Gehm's Corollary to Clarke's Third Law > > > > > >[[alternative HTML version deleted]]