[R] ggridges help

Wed Oct 18 01:29:55 CEST 2017

Perfect,  thank you.  

I find the Unix style help usual in R is really only helpful once you know what everything is doing.  That makes a good vignette, that shows what all of the options do in a careful way,  really important. 

Thanks again.

-Roy

> On Oct 17, 2017, at 2:01 PM, William Dunlap <wdunlap at tibco.com> wrote:
> 
> The min_height = -0.25 is there to make it show cycle values down to -1/4.  You may want to change it to -1 so it shows more of the cycle values.
> 
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
> 
> On Tue, Oct 17, 2017 at 1:26 PM, Roy Mendelssohn - NOAA Federal <roy.mendelssohn at noaa.gov> wrote:
> yes, thanks,  and I was getting close to that.  One thing I found is the manual says the height is the distance above the y-line,  which should be, but doesn't have to be positive.  In fact,  the time series are  estimates of a cycle,  and has negative values,  which unfortunately are not included in my sub-sample.  And the negative values are not handled properly (the series disappears for the negative values)
> 
> Also,  maybe it is my bad eyesight,  but in examples of the older, deprecated ggjoy package,  there seem to be a slight offset added to the depth effect,  which doesn't appear to be the case now, or am I missing something.  There is this in the manual:
> 
> 
> > position
> > Position adjustment, either as a string, or the result of a call to a position adjustment function.
> 
> I assume this refers to the ggplot2 position adjustments.  Would one of those calls have that effect?
> 
> Thanks,
> 
> -Roy
> 
> 
> 
> 
> > On Oct 17, 2017, at 1:09 PM, William Dunlap <wdunlap at tibco.com> wrote:
> >
> > Does the following work for you?
> >
> >    ggplot2::ggplot(plotFrame, aes(x = time, y = depth, height = cycle, group = depth)) + ggridges::geom_ridgeline(fill="red", min_height=-0.25)
> >
> >
> > Bill Dunlap
> > TIBCO Software
> > wdunlap tibco.com
> >
> > On Tue, Oct 17, 2017 at 12:43 PM, Roy Mendelssohn - NOAA Federal <roy.mendelssohn at noaa.gov> wrote:
> > I have tried:
> >
> > ggplot(plotFrame, aes(x = time, y = cycle, height = cycle, group = depth)) + geom_ridgeline()
> > ggplot(plotFrame, aes(x = time, y = depth, height = cycle, group = depth)) + geom_ridgeline()
> > ggplot(plotFrame, aes(x = time, y = depth, group = depth)) + geom_density_ridges()
> >
> > none are producing a plot that was a ridgeline for each depth showing the time series at that depth.  The plot should be like the geom_line plot,  but as a ridgeline for each depth.
> >
> > -Roy
> >
> > > On Oct 17, 2017, at 12:39 PM, Bert Gunter <bgunter.4567 at gmail.com> wrote:
> > >
> > > ...and your question is...?
> > > ... and the code you tried that didn't work was?
> > >
> > > Bert
> > >
> > >
> > > On Oct 17, 2017 12:22 PM, "Roy Mendelssohn - NOAA Federal" <roy.mendelssohn at noaa.gov> wrote:
> > > Hi All:
> > >
> > > I am just not understanding ggridges.  The data I have are time series at different depths in the ocean.  I want to make a joy plot of the time series by depth.
> > >
> > > If I was just doing a ggplot2 line plot I would be doing:
> > >
> > > ggplot(plotFrame, aes(x = time, y = cycle, group = depth)) + geom_line()
> > >
> > > but translating that to ggridges has not worked right.  Below is the result from dput() of a simplified data frame that has 3 depths and 2 years of monthly data.  (In fact I have  20 depths and 30  years of monthly data).   The command above will work with this data frame.
> > >
> > > Thanks for any help.
> > >
> > > -Roy
> > >
> > > >dput(plotFrame)
> > > structure(list(time = structure(c(719236800, 721915200, 724507200,
> > > 727185600, 729777600, 732283200, 734961600, 737553600, 740232000,
> > > 742824000, 745502400, 748180800, 750772800, 753451200, 756043200,
> > > 758721600, 761313600, 763819200, 766497600, 769089600, 771768000,
> > > 774360000, 777038400, 779716800, 719236800, 721915200, 724507200,
> > > 727185600, 729777600, 732283200, 734961600, 737553600, 740232000,
> > > 742824000, 745502400, 748180800, 750772800, 753451200, 756043200,
> > > 758721600, 761313600, 763819200, 766497600, 769089600, 771768000,
> > > 774360000, 777038400, 779716800, 719236800, 721915200, 724507200,
> > > 727185600, 729777600, 732283200, 734961600, 737553600, 740232000,
> > > 742824000, 745502400, 748180800, 750772800, 753451200, 756043200,
> > > 758721600, 761313600, 763819200, 766497600, 769089600, 771768000,
> > > 774360000, 777038400, 779716800), class = c("POSIXct", "POSIXt"
> > > ), tzone = "UTC"), depth = structure(c(1L, 1L, 1L, 1L, 1L, 1L,
> > > 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
> > > 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
> > > 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L,
> > > 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
> > > 3L, 3L), .Label = c("20", "40", "60"), class = "factor"), cycle = structure(c(-0.164397110685046,
> > > -0.0639063592004652, -0.124275650584243, 0.232340199700421, 0.23265929828899,
> > > 0.452800479990173, 0.631515844862171, 0.708775442811806, 0.402797787246307,
> > > 0.540279471159411, 0.625583653374072, 0.607609707505232, 0.789645459141814,
> > > 0.57943178332249, 0.395406041578379, 0.278792362706845, 0.000158405680203533,
> > > 0.0618374997078718, 0.0942838757427736, 0.046510899158667, 0.136800366664298,
> > > 0.165118554160811, 0.228812312665972, -0.225383761996565, -0.204115732057999,
> > > -0.0883683879679482, -0.135111844938738, 0.147562070872115, 0.198086355354394,
> > > 0.386803300687593, 0.684023051288189, 0.69669009829253, 0.381213154479,
> > > 0.550118050327324, 0.641294267691433, 0.614909878956221, 0.772779409518665,
> > > 0.581967160929841, 0.381662488154885, 0.293380662335543, 0.0391733417449068,
> > > -0.0844674860904995, 0.163695040677223, 0.0444585016269223, 0.130561029192561,
> > > 0.180784990884611, 0.242929491090375, -0.126543843540014, -0.112781525045155,
> > > -0.1803388763034, -0.0939120153437669, 0.150968491445835, 0.0992298571202001,
> > > 0.289294645512006, 0.540517483378127, 0.625091194385051, 0.432224338078479,
> > > 0.504654513110009, 0.62584673393424, 0.56834612321311, 0.789331138620147,
> > > 0.6389908671341, 0.45156693996368, 0.412578785088203, 0.212440848202924,
> > > 0.146392303930216, 0.654494252844301, 0.470248736982212, 0.239891529116349,
> > > 0.200137949677769, 0.2858429346658, -0.121094155739595), .Dim = 72L)), .Names = c("time",
> > > "depth", "cycle"), row.names = c(NA, -72L), class = "data.frame")
> > >
> > > **********************
> > > "The contents of this message do not reflect any position of the U.S. Government or NOAA."
> > > **********************
> > > Roy Mendelssohn
> > > Supervisory Operations Research Analyst
> > > NOAA/NMFS
> > > Environmental Research Division
> > > Southwest Fisheries Science Center
> > > ***Note new street address***
> > > 110 McAllister Way
> > > Santa Cruz, CA 95060
> > > Phone: (831)-420-3666
> > > Fax: (831) 420-3980
> > > e-mail: Roy.Mendelssohn at noaa.gov www: http://www.pfeg.noaa.gov/
> > >
> > > "Old age and treachery will overcome youth and skill."
> > > "From those who have been given much, much will be expected"
> > > "the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
> > >
> > > ______________________________________________
> > > 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.
> >
> > **********************
> > "The contents of this message do not reflect any position of the U.S. Government or NOAA."
> > **********************
> > Roy Mendelssohn
> > Supervisory Operations Research Analyst
> > NOAA/NMFS
> > Environmental Research Division
> > Southwest Fisheries Science Center
> > ***Note new street address***
> > 110 McAllister Way
> > Santa Cruz, CA 95060
> > Phone: (831)-420-3666
> > Fax: (831) 420-3980
> > e-mail: Roy.Mendelssohn at noaa.gov www: http://www.pfeg.noaa.gov/
> >
> > "Old age and treachery will overcome youth and skill."
> > "From those who have been given much, much will be expected"
> > "the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
> >
> > ______________________________________________
> > 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.
> >
> 
> **********************
> "The contents of this message do not reflect any position of the U.S. Government or NOAA."
> **********************
> Roy Mendelssohn
> Supervisory Operations Research Analyst
> NOAA/NMFS
> Environmental Research Division
> Southwest Fisheries Science Center
> ***Note new street address***
> 110 McAllister Way
> Santa Cruz, CA 95060
> Phone: (831)-420-3666
> Fax: (831) 420-3980
> e-mail: Roy.Mendelssohn at noaa.gov www: http://www.pfeg.noaa.gov/
> 
> "Old age and treachery will overcome youth and skill."
> "From those who have been given much, much will be expected"
> "the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
> 
> 

**********************
"The contents of this message do not reflect any position of the U.S. Government or NOAA."
**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: Roy.Mendelssohn at noaa.gov www: http://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected" 
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.