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.
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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