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>
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
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).