On Sat, Sep 29, 2012 at 7:32 AM, ilai <ke...@math.montana.edu> wrote:
> On Fri, Sep 28, 2012 at 11:03 PM, Elaine Kuo <elaine.kuo...@gmail.com>wrote: > >> Hello >> >> Thanks again. >> >> I got the attached graph >> Unsure why the color is still inconsistent. >> Please kindly share with your R version. >> > > It is not my version you need to worry about, but your own... > Post the following outputs (without the prompt): > > > sessionInfo() > > ls(pat = 'bwplot' ) > > str(dataN) > > The complete code you run on a vanilla session (at this point I can only > guess you changed mine somehow) > > dput(dataN) > > That will be better than having me or anyone in R-help play "guess how I > got this plot". > > > > > >> Also, I want to add one line in the command. >> levels(dataN$Diet_B) <- diet.code >> diet.code <- c("Herbivore_t", "Herbivore_w", "Nectivore", "Frugivore", >> "Granivore", >> "Scavenger", "Carnivore", >> "Insectivore_t", "Insectivore_w", "Insectivore_a", >> "Molluscivore", "Crustacean feeder", "Omnivore") >> >> Please kindly help how to make the levels vertical instead of horizontal. >> >> Elaine >> >> On Sat, Sep 29, 2012 at 12:28 PM, ilai <ke...@math.montana.edu> wrote: >> >>> Not sure why this is going wrong for you. >>> Copy paste AS IS the following to your console in the directory >>> containing for_lattice.csv >>> >>> str(dataN <- read.csv('for_lattice.csv')[,2:3]) >>> dataN$Diet_B <- factor(dataN$Diet_B) >>> >>> Diet.colors <- c("forestgreen", "darkgreen","chocolate1","darkorange2", >>> "sienna2","red2","firebrick3","saddlebrown","coral4","chocolate4","darkblue","navy","grey38") >>> require(lattice) >>> bwplot(MS_midpoint_lat~Diet_B,dataN,pch='|', >>> par.settings = list( >>> plot.symbol =list(col = rep(Diet.colors,c(1,0,0,1,0,0,3,6,1,0,2,0,1)) ), >>> box.dot =list(col=Diet.colors), >>> box.rectangle=list(col=Diet.colors), >>> box.umbrella=list(lty=1,col=Diet.colors))) >>> >>> Are you seeing this ? >>> >>> >>> >>> On Fri, Sep 28, 2012 at 7:06 PM, Elaine Kuo <elaine.kuo...@gmail.com>wrote: >>> >>>> Hello >>>> >>>> Thanks for the quick response. >>>> >>>> For your code, >>>> the result is attached Q1. >>>> >>>> Please kindly help with the same color of box line and whisker just >>>> like box 1 of green. >>>> >>>> I attached my data and plot result (Q2). >>>> Please kindly help change the median from "I" to "-." >>>> >>>> Thanks a lot. >>>> >>>> Elaine >>>> >>>> >>>> On Sat, Sep 29, 2012 at 8:21 AM, ilai <ke...@math.montana.edu> wrote: >>>> >>>>> Me again... >>>>> Sorry I just noticed you did provide reproducible code in your >>>>> original. To get your plot: >>>>> >>>>> require(lattice) >>>>> set.seed(5) >>>>> >>>>> Diet.colors <- c("forestgreen", >>>>> "darkgreen","chocolate1","darkorange2", >>>>> "sienna2","red2","firebrick3","saddlebrown","coral4","chocolate4","darkblue","navy","grey38") >>>>> bwplot(rgamma(20*13,1,.1)~gl(13,20), pch = "|", >>>>> par.settings = list( >>>>> plot.symbol =list(col = rep(Diet.colors,c(0,1,1,3,1,0,3,0,0,1,1,1,0)) >>>>> ), >>>>> box.dot =list(col=Diet.colors), >>>>> box.rectangle=list(col=Diet.colors), >>>>> box.umbrella=list(lty=1,col=Diet.colors))) >>>>> >>>>> The box arguments set the box parameters (lty,col etc.) but the >>>>> plot.symbol sets the outliers parameters (again pch, col etc.). Note the >>>>> rep vector! it is because box 1 doesn't have an outlier, but box 4 has 3. >>>>> You will need to construct it based on your real data or the colors will >>>>> be >>>>> off. >>>>> >>>>> Cheers >>>>> >>>>> >>>>> On Fri, Sep 28, 2012 at 5:55 PM, ilai <ke...@math.montana.edu> wrote: >>>>> >>>>>> >>>>>> On Fri, Sep 28, 2012 at 4:17 PM, Elaine Kuo >>>>>> <elaine.kuo...@gmail.com>wrote: >>>>>> >>>>>>> Hello Ilai, >>>>>>> >>>>>>> Thank you for the response. >>>>>>> It did help a lot. >>>>>>> >>>>>>> However, a beginner to lattice has three questions. >>>>>>> >>>>>>> Q1 >>>>>>> >>>>>>> Please kindly explain why "in this case OP is using it with no "at" >>>>>>> argument,"" >>>>>>> >>>>>> >>>>>> Quoting from ?panel.bwplot.intermediate.hh (i.e. help file) >>>>>> >>>>>> " >>>>>> Description: >>>>>> >>>>>> Panel function for bwplot that give the user control over the >>>>>> placement of the boxes. When used with a positioned factor, the >>>>>> boxes are placed according to the position associated with the >>>>>> factor. >>>>>> " >>>>>> >>>>>> You did not supply a position factor ("at" argument) so all you are >>>>>> doing is using HH::panel.bwplot instead of the original >>>>>> lattice::panel.bwplot. This would have been OK but seems like there were >>>>>> some changes made to panel.bwplot.intermediate.hh so it doesn't give you >>>>>> what you want >>>>>> >>>>>> so it is possible to display the median and the outliers with >>>>>>> different pch? >>>>>>> >>>>>> >>>>>> Did you run my examples ? I see the attached for the second. Is this >>>>>> not what you want ? if you did run my examples and see something else, >>>>>> try >>>>>> again in a new R session with only lattice loaded. Let me know. >>>>>> >>>>>> >>>>>>> >>>>>>> Q2. >>>>>>> what is the relationship between package "HH" and graphic-drawing? >>>>>>> I checked ??HH and found little explanation on its function of >>>>>>> graphic-drawing. >>>>>>> >>>>>> >>>>>> Intro to R and many other web resources/books will explain the R >>>>>> architecture. In general packages hold functions, and there is no problem >>>>>> to have dependencies - i.e. function in one package calling a function >>>>>> from >>>>>> another. For example lattice has a bunch of plotting tools. HH calls one >>>>>> of >>>>>> them (panel.bwplot) and modifies it a little to get some effect (non auto >>>>>> placement of boxes). You can use whichever package::function you want or >>>>>> even build your local copy of the function. Richard can correct me and >>>>>> tell you more but I think HH is mostly a collection of his such local >>>>>> modifications. >>>>>> >>>>>> >>>>>>> >>>>>>> Q3 >>>>>>> >>>>>>> Please kindly advise how to make outliers empty circle (pch=2) in >>>>>>> this case as the code below. >>>>>>> >>>>>> >>>>>> This is not a reproducible example. I don't have dataN. See my answer >>>>>> to Q1. Replace the formula of my (reproducible) code with yours and add >>>>>> the >>>>>> fancy axis annotations etc.. If you are still not getting it, in the >>>>>> console type >>>>>> dput(dataN) >>>>>> >>>>>> copy paste the output to your reply. >>>>>> >>>>>> HTH >>>>>> >>>>>> >>>>>> >>>>>>> Thank you. >>>>>>> >>>>>>> code >>>>>>> >>>>>>> Diet.colors <- >>>>>>> c("forestgreen","darkgreen","chocolate1","darkorange2","sienna2", >>>>>>> >>>>>>> "red2","firebrick3","saddlebrown","coral4","chocolate4","darkblue","navy","grey38") >>>>>>> >>>>>>> levels(dataN$Diet_B) <- diet.code >>>>>>> >>>>>>> >>>>>>> bwplot(MS_midpoint_lat~Diet_B, data=dataN, >>>>>>> xlab=list("Diet of Breeding Ground", cex = 1.4), >>>>>>> ylab = list("Latitudinal Midpoint Breeding Ground ",cex = 1.4), >>>>>>> lwd=1.5, >>>>>>> cex.lab=1.4, cex.axis=1.2, >>>>>>> font.axis=2, >>>>>>> cex=1.5, >>>>>>> las=1, >>>>>>> panel=panel.bwplot.intermediate.hh, >>>>>>> bty="l", >>>>>>> col=Diet.colors, >>>>>>> pch=rep("l",13), >>>>>>> scales=list(x=list(rot=90)), >>>>>>> par.settings=list(plot.symbol = list(pch = 2, cex = >>>>>>> 2),box.umbrella=list(lty=1))) >>>>>>> >>>>>>> Elaine >>>>>>> >>>>>>> >>>>>>> On Sat, Sep 29, 2012 at 2:44 AM, ilai <ke...@math.montana.edu>wrote: >>>>>>> >>>>>>>> On Fri, Sep 28, 2012 at 6:57 AM, Richard M. Heiberger < >>>>>>>> r...@temple.edu> wrote: >>>>>>>> >>>>>>>>> Elaine, >>>>>>>>> >>>>>>>>> For panel.bwplot you see that the central dot and the outlier dots >>>>>>>>> are >>>>>>>>> controlled by >>>>>>>>> the same pch argument. >>>>>>>> >>>>>>>> >>>>>>>> ??? I don't think so... >>>>>>>> >>>>>>>> bwplot(rgamma(20,.1,1)~gl(2,10), pch=rep(17,2), >>>>>>>> panel = lattice::panel.bwplot) >>>>>>>> >>>>>>>> I think you mean panel.bwplot.intermidiate.hh ? >>>>>>>> >>>>>>>> BTW thank you for the useful HH package but in this case OP is >>>>>>>> using it with no "at" argument, so why not >>>>>>>> >>>>>>>> Diet.colors <- c("forestgreen", >>>>>>>> "darkgreen","chocolate1","darkorange2", >>>>>>>> "sienna2","red2","firebrick3","saddlebrown","coral4","chocolate4","darkblue","navy","grey38") >>>>>>>> bwplot(rgamma(20*13,1,.1)~gl(13,20), >>>>>>>> fill = Diet.colors, pch = "|", >>>>>>>> par.settings = list(box.umbrella=list(lty=1))) >>>>>>>> >>>>>>>> cheers >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> I initially set the pch="|" to match your first >>>>>>>>> example with the horizontal >>>>>>>>> indicator for the median. I would be inclined to use the default >>>>>>>>> circle >>>>>>>>> for the outliers and >>>>>>>>> therefore also for the median. >>>>>>>>> >>>>>>>>> Rich >>>>>>>>> >>>>>>>>> On Fri, Sep 28, 2012 at 7:13 AM, Sarah Goslee < >>>>>>>>> sarah.gos...@gmail.com>wrote: >>>>>>>>> >>>>>>>>> > I would guess that if you find the bit that says pch="|" and >>>>>>>>> change it to >>>>>>>>> > pch=1 it will solve your question, and that reading ?par will >>>>>>>>> tell you why. >>>>>>>>> > >>>>>>>>> > Sarah >>>>>>>>> > >>>>>>>>> > On Thursday, September 27, 2012, Elaine Kuo wrote: >>>>>>>>> > >>>>>>>>> > > Hello >>>>>>>>> > > >>>>>>>>> > > This is Elaine. >>>>>>>>> > > >>>>>>>>> > > I am using package lattice to generate boxplots. >>>>>>>>> > > Using Richard's code, the display was almost perfect except >>>>>>>>> the outlier >>>>>>>>> > > shape. >>>>>>>>> > > Based on the following code, the outliers are vertical lines. >>>>>>>>> > > However, I want the outliers to be empty circles. >>>>>>>>> > > Please kindly help how to modify the code to change the >>>>>>>>> outlier shapes. >>>>>>>>> > > Thank you. >>>>>>>>> > > >>>>>>>>> > > code >>>>>>>>> > > package (lattice) >>>>>>>>> > > >>>>>>>>> > > dataN <- data.frame(GE_distance=rnorm(260), >>>>>>>>> > > >>>>>>>>> > > Diet_B=factor(rep(1:13, each=20))) >>>>>>>>> > > >>>>>>>>> > > Diet.colors <- c("forestgreen", >>>>>>>>> "darkgreen","chocolate1","darkorange2", >>>>>>>>> > > >>>>>>>>> > > >>>>>>>>> "sienna2","red2","firebrick3","saddlebrown","coral4", >>>>>>>>> > > >>>>>>>>> > > "chocolate4","darkblue","navy","grey38") >>>>>>>>> > > >>>>>>>>> > > levels(dataN$Diet_B) <- Diet.colors >>>>>>>>> > > >>>>>>>>> > > bwplot(GE_distance ~ Diet_B, data=dataN, >>>>>>>>> > > >>>>>>>>> > > xlab=list("Diet of Breeding Ground", cex = 1.4), >>>>>>>>> > > >>>>>>>>> > > ylab = list( >>>>>>>>> > > >>>>>>>>> > > "Distance between Centers of B and NB Range (1000 >>>>>>>>> km)", >>>>>>>>> > > >>>>>>>>> > > cex = 1.4), >>>>>>>>> > > >>>>>>>>> > > panel=panel.bwplot.intermediate.hh, >>>>>>>>> > > >>>>>>>>> > > col=Diet.colors, >>>>>>>>> > > >>>>>>>>> > > pch=rep("|",13), >>>>>>>>> > > >>>>>>>>> > > scales=list(x=list(rot=90)), >>>>>>>>> > > >>>>>>>>> > > par.settings=list(box.umbrella=list(lty=1))) >>>>>>>>> > > >>>>>>>>> > > [[alternative HTML version deleted]] >>>>>>>>> > > >>>>>>>>> > > ______________________________________________ >>>>>>>>> > > R-help@r-project.org <javascript:;> 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. >>>>>>>>> > > >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > -- >>>>>>>>> > Sarah Goslee >>>>>>>>> > http://www.stringpage.com >>>>>>>>> > http://www.sarahgoslee.com >>>>>>>>> > http://www.functionaldiversity.org >>>>>>>>> > >>>>>>>>> > [[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. >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> > [[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.