[R] [FORGED] Re: Quantile Density Contours

PIKAL Petr
Thu, 28 Mar 2019 06:26:29 -0000

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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