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() > 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.