[R] [FORGED] Re: Quantile Density Contours

Bernard Comcast
Thu, 28 Mar 2019 11:56:27 -0000

Thanks Petr

Bernard
Sent from my iPhone so please excuse the spelling!"

> On Mar 28, 2019, at 2:26 AM, PIKAL Petr <petr.pikal at precheza.cz>
wrote:
>
> Hallo Bernard
>
> I did not follow all emails in this thread but it seems to me that your
request is similar to Bioconductor packages dealing with Flow Cytometry data.
>
> Especially flowViz package is designed to visualise such data.
>
> Cheers
> Petr
>
>
>> -----Original Message-----
>> From: R-help <r-help-bounces at r-project.org> On Behalf Of
Bernard McGarvey
>> Sent: Wednesday, March 27, 2019 9:55 PM
>> To: Paul Murrell <paul at stat.auckland.ac.nz>; John Kane
>> <jrkrideau at gmail.com>
>> Cc: R. Help Mailing List <r-help at r-project.org>
>> Subject: Re: [R] [FORGED] Re: Quantile Density Contours
>>
>> If I understand correctly the ContourLines function gives you the
contour lines
>> when you put in the data. But before this I need to data to put into
that
>> function. I think this is something like a 2D CDF of the data that then
leads to
>> the 2D quantiles but I am not 100% sure. What I am basically looking
for is the
>> 2D curve that encloses say 95% of the data in a similar fashion to a 1D
quantile
>> where the quantile represents the value that x% of the data is below. I
think
>> what I am looking for is the 2D bivariate version of the 1D quantile
plot (where
>> the quantile value is plotted vs the % value).
>>
>> I hope this makes some sense.
>>
>> Bernard McGarvey
>>
>>
>> Director, Fort Myers Beach Lions Foundation, Inc.
>>
>>
>> Retired (Lilly Engineering Fellow).
>>
>>
>>> On March 27, 2019 at 3:57 PM Paul Murrell <paul at
stat.auckland.ac.nz>
>> wrote:
>>>
>>>
>>>
>>> Are you looking for the contourLines() function ?
>>>
>>> Paul
>>>
>>>> On 28/03/19 8:37 AM, Bernard McGarvey wrote:
>>>> John, I have attached a pdf of the plot. Hopefully you can read
this.
>>>>
>>>> If I understand correctly, this plot is basically the 2-D
version of the 1-D
>> quantile plot.
>>>>
>>>> Thanks
>>>>
>>>> Bernard McGarvey
>>>>
>>>>
>>>> Director, Fort Myers Beach Lions Foundation, Inc.
>>>>
>>>>
>>>> Retired (Lilly Engineering Fellow).
>>>>
>>>>
>>>>> On March 27, 2019 at 7:44 AM John Kane <jrkrideau at
gmail.com> wrote:
>>>>>
>>>>>
>>>>> The figure did not get  through. Perhaps try a pdf?
>>>>>
>>>>> On Tue, 26 Mar 2019 at 13:41, Bernard McGarvey
>>>>> <mcgarvey.bernard at comcast.net> wrote:
>>>>>>
>>>>>> I want to see if I can reproduce the plot below in R.
If I
>>>>>> understand it correctly, i takes my bivariate data and
creates
>>>>>> quantile density contours. My interpretation of these
contours is
>>>>>> that they enclose a certain % of the total data. I am
using the
>>>>>> bkde2D function in library KernSmooth which gives
density values
>>>>>> that can be plotted on a contour plot but I would like
the curves
>>>>>> that enclose a given % of the data, if that is possible
>>>>>>
>>>>>>
>>>>>> Thanks
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Bernard McGarvey
>>>>>>
>>>>>> Director, Fort Myers Beach Lions Foundation, Inc.
>>>>>>
>>>>>> Retired (Lilly Engineering Fellow).
>>>>>>
>>>>>>
>>>>>> ______________________________________________
>>>>>> 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.
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> John Kane
>>>>> Kingston ON Canada
>>>>>
>>>>> ______________________________________________
>>>>> 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.
>>>
>>> --
>>> Dr Paul Murrell
>>> Department of Statistics
>>> The University of Auckland
>>> Private Bag 92019
>>> Auckland
>>> New Zealand
>>> 64 9 3737599 x85392
>>> paul at stat.auckland.ac.nz
>>> http://www.stat.auckland.ac.nz/~paul/
>>
>> ______________________________________________
>> 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.
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