Hi,
I have a matrix of data, with the rows representing observations and the
columns representing various values that the observation can take on.
In other words, each row can be thought of as a sampling of the density
function/histogram associated with the range of values for that
observation.
I'd like to graph these with a shaded color, rather than as lines. So a
given observation would have the darkest shade at the mean and the
shading would lighten for values that approached the tails. In a sense
this is like a ribbon chart, but where there are many confidence bands.
I think the example near the bottom of this page
http://bconnelly.net/2013/10/creating-colorblind-friendly-figures/
starts to get at what I want. But when I tried to get a ribbon, I get
an error message saying that "Error: Aesthetics can not vary with a
ribbon"
Can anyone point me to an example that accomplishes my task, or give me
some ideas as to how to code this?
Below is a reproducible dataset and the code I ran that generated the
above error. And apologies in advance if I have overlooked some obvious
source - I'm not exactly sure what keywords to search for.
Regards,
Matt
testdataset <- structure(c(0.703482475602795, 0.708141442616021,
0.696373713631662,
0.670284015871304, 0.675183812793659,
0.690440437259122, 0.717483375152826,
0.775328205198994, 0.848374059782512,
0.869939471712489, 0.86329313061477,
0.842138830353923, 0.819853961383293,
0.808038546509378, 0.826626282345039,
0.855428819162732, 0.873943618483253,
0.906412218904192, 0.95345525957727,
0.941481792397259, 0.923791753474186,
0.909206164221341, 0.847283523824235,
0.774333551860785, 0.723440114819687,
0.653247411286407, 0.585889004137383,
0.516531935718585, 0.458855598305008,
0.422596378188962, 0.385800210249005,
0.363663809831211, 0.703482475602795,
0.708055808109959, 0.696379276680681,
0.686643131558789, 0.702628930558265,
0.736010723583024, 0.790795207667811,
0.843997296035071, 0.872447231982615,
0.876357159885425, 0.852095141662599,
0.815122741092172, 0.759163100114952,
0.737079598996168, 0.755626127703219,
0.76375495269533, 0.757290640161052,
0.754301244147121, 0.738872719902144,
0.712590028244082, 0.707690675037336,
0.707234385372842, 0.708720518303698,
0.723271948541464, 0.738173079905318,
0.772161522113349, 0.776237486574842,
0.775666977944939, 0.764229462885737,
0.758916671383124, 0.742887393474484,
0.741362343479079, 0.703482475602795,
0.70722192044612, 0.694934601341247,
0.675623005679584, 0.67355293987199,
0.67514195581405, 0.701338223542176,
0.770084545123592, 0.826615555391194,
0.815331595124185, 0.801265437257298,
0.768736104243487, 0.698903427959817,
0.654393072393584, 0.646507677289504,
0.606308031283892, 0.574521529688064,
0.550931914275617, 0.518538683619987,
0.495773346159491, 0.482784058725618,
0.473031502762785, 0.462940836756943,
0.455472910452526, 0.457374752189383,
0.468449683385787, 0.469177346159405,
0.47981744053419, 0.500517935694715,
0.521161553352487, 0.538278248678118,
0.545834896270532, 0.703482475602795,
0.707475643569319, 0.695699528962731,
0.695460540915422, 0.705063229294573,
0.694190083263775, 0.676451221936696,
0.661139999162065, 0.627150885842318,
0.592467979293877, 0.556197511727567,
0.524883713023224, 0.484571801496662,
0.427784904562, 0.370137413134906,
0.331233866457343, 0.292181528642806,
0.265504971226103, 0.239129968439056,
0.21258454640671, 0.184521419432522,
0.160633576032345, 0.135729972994914,
0.115111431576686, 0.0933784744252792,
0.0672765522562478, 0.0397992726679255,
0.0118179662548541, NA, NA, NA, NA,
0.703482475602795, 0.70791132542366,
0.696508162877812, 0.672357035115831,
0.679831378223931, 0.702075998432084,
0.736057349706643, 0.759252979404642,
0.739391321260192, 0.706608353324493,
0.653481111693474, 0.607986236497692,
0.600942686427268, 0.602450590412635,
0.594096281507138, 0.598414292518021,
0.570859444977738, 0.50462737404968,
0.441225469913529, 0.37010584373766,
0.299554326292306, 0.250957120974181,
0.231147047662909, 0.218081437060998,
0.209354124252359, 0.212236940966109,
0.213898409405384, 0.200693009702681,
0.189880443626695, 0.175663436717225,
0.160910269517771, 0.14423774751828,
0.703482475602795, 0.707648742091919,
0.696092540716741, 0.656540853310246,
0.6051367218461, 0.591695064299013,
0.596015810648035, 0.603800534715597,
0.630728546677123, 0.658732672149451,
0.660216960664134, 0.675188962779905,
0.680940355728037, 0.677371529164165,
0.678862966955137, 0.706307948099043,
0.72103331978575, 0.71201796002067,
0.695266699409018, 0.685297231486624,
0.661576951062559, 0.643301885602357,
0.619830526453808, 0.608129873046412,
0.594283830084397, 0.562317115717112,
0.530350595536459, 0.506782526041746,
0.485311767855001, 0.473335687828819,
0.47767850215973, 0.47780651839627,
0.703482475602795, 0.708970958906805,
0.697551150784402, 0.661080016538957,
0.61232038566617, 0.587787379274781,
0.593431699246192, 0.585207322444761,
0.568559116457046, 0.548048255621954,
0.530114701694855, 0.534118004338362,
0.551070523651917, 0.575923824458594,
0.601811119913484, 0.599679943614892,
0.571040665848032, 0.537593347467274,
0.517448133546794, 0.509401266935977,
0.506839184709813, 0.513795796376072,
0.538416419444161, 0.54431580354862,
0.533416582151419, 0.536830327067308,
0.536462655629334, 0.513629165635279,
0.478995218355945, 0.438690505845544,
0.382567436102273, 0.34023179757446,
0.703482475602795, 0.708469004078862,
0.697978508894162, 0.676172179276398,
0.653999136795877, 0.621901773418305,
0.611086726778221, 0.593857278888487,
0.59772372401201, 0.615523307201519,
0.639972290824288, 0.642201950188424,
0.640462288885887, 0.599634050862654,
0.556922658075191, 0.51984992524725,
0.500551878868105, 0.481116358620079,
0.46280476578578, 0.439079916934238,
0.426481043460678, 0.4046073777228,
0.384894885963074, 0.387418227322783,
0.397735327855843, 0.382421337902373,
0.364609477937235, 0.351141834403433,
0.326023299419572, 0.298998310511409,
0.279388702747555, 0.265729633371279,
0.703482475602795, 0.708084110634261,
0.695308105608089, 0.680512620916581,
0.674409687648891, 0.64479397663385,
0.611185461407328, 0.574633943767944,
0.531967082066137, 0.509238294683539,
0.539380037981121, 0.605934156503129,
0.67139250700667, 0.692111261722321,
0.681033453581129, 0.649259774238939,
0.61340010828123, 0.601868728090964,
0.626623248125788, 0.630474601620122,
0.632877115180945, 0.622655315896617,
0.602457206226614, 0.577755838513823,
0.575613491077747, 0.56693811567409,
0.538199408312755, 0.508731518312269,
0.488361667141151, 0.462965384850233,
0.438776128537772, 0.433205440295598,
0.703482475602795, 0.708955081210283,
0.696337276771488, 0.675657944024044,
0.682199731001736, 0.713302322144747,
0.780735831443758, 0.836330924875064,
0.920042864888473, 0.993749005071184,
1.09383447176433, 1.13919188883409,
1.17120759930688, 1.20149479327377,
1.21627978424244, 1.16585978639785,
1.11758399725948, 1.04238685207932,
0.937208207066276, 0.862384770704829,
0.774099878399983, 0.701556273005073,
0.670583202198987, 0.686968300073611,
0.732378201300416, 0.820191766252091,
0.855392362283012, 0.845365464014818,
0.803317719342587, 0.757849795095728,
0.711624608771727, 0.674398052370244), .Dim =
c(32L, 10L))
matplot(testdataset, type = 'l', las = 1, xlab = 'x values',
ylab = 'y values', main = 'title - testdataset')
library(ggplot2,RColorBrewer,reshape2)
testdataset[ is.na(testdataset) ] <- 0
testdataset2 <- melt(testdataset)
ggplot(testdataset2, aes(x=Var1,y=factor(value))) +
stat_density(aes(fill=..density..), position="identity") +
scale_fill_gradientn(colours=brewer.pal(n=8, name="PuBuGn"))
Does this resemble what you're after?
library(reshape2)
tst <- melt(testdataset)
library(ggplot2)
ggplot(tst, aes(x=Var1, y=Var2, fill=value)) +
geom_tile() +
scale_fill_gradient2(low="white",
high="white",
mid=scales::muted("blue"),
midpoint=0.6148377)
On Wed, Sep 24, 2014 at 10:26 AM, <matt at considine.net>
wrote:> Hi,
> I have a matrix of data, with the rows representing observations and the
> columns representing various values that the observation can take on. In
> other words, each row can be thought of as a sampling of the density
> function/histogram associated with the range of values for that
observation.
>
> I'd like to graph these with a shaded color, rather than as lines. So
a
> given observation would have the darkest shade at the mean and the shading
> would lighten for values that approached the tails. In a sense this is
like
> a ribbon chart, but where there are many confidence bands.
>
> I think the example near the bottom of this page
> http://bconnelly.net/2013/10/creating-colorblind-friendly-figures/
> starts to get at what I want. But when I tried to get a ribbon, I get an
> error message saying that "Error: Aesthetics can not vary with a
ribbon"
>
> Can anyone point me to an example that accomplishes my task, or give me
some
> ideas as to how to code this?
>
> Below is a reproducible dataset and the code I ran that generated the above
> error. And apologies in advance if I have overlooked some obvious source -
> I'm not exactly sure what keywords to search for.
>
> Regards,
> Matt
>
> testdataset <- structure(c(0.703482475602795, 0.708141442616021,
> 0.696373713631662,
> 0.670284015871304, 0.675183812793659,
> 0.690440437259122, 0.717483375152826,
> 0.775328205198994, 0.848374059782512,
> 0.869939471712489, 0.86329313061477,
> 0.842138830353923, 0.819853961383293,
> 0.808038546509378, 0.826626282345039,
> 0.855428819162732, 0.873943618483253,
> 0.906412218904192, 0.95345525957727,
> 0.941481792397259, 0.923791753474186,
> 0.909206164221341, 0.847283523824235,
> 0.774333551860785, 0.723440114819687,
> 0.653247411286407, 0.585889004137383,
> 0.516531935718585, 0.458855598305008,
> 0.422596378188962, 0.385800210249005,
> 0.363663809831211, 0.703482475602795,
> 0.708055808109959, 0.696379276680681,
> 0.686643131558789, 0.702628930558265,
> 0.736010723583024, 0.790795207667811,
> 0.843997296035071, 0.872447231982615,
> 0.876357159885425, 0.852095141662599,
> 0.815122741092172, 0.759163100114952,
> 0.737079598996168, 0.755626127703219,
> 0.76375495269533, 0.757290640161052,
> 0.754301244147121, 0.738872719902144,
> 0.712590028244082, 0.707690675037336,
> 0.707234385372842, 0.708720518303698,
> 0.723271948541464, 0.738173079905318,
> 0.772161522113349, 0.776237486574842,
> 0.775666977944939, 0.764229462885737,
> 0.758916671383124, 0.742887393474484,
> 0.741362343479079, 0.703482475602795,
> 0.70722192044612, 0.694934601341247,
> 0.675623005679584, 0.67355293987199,
> 0.67514195581405, 0.701338223542176,
> 0.770084545123592, 0.826615555391194,
> 0.815331595124185, 0.801265437257298,
> 0.768736104243487, 0.698903427959817,
> 0.654393072393584, 0.646507677289504,
> 0.606308031283892, 0.574521529688064,
> 0.550931914275617, 0.518538683619987,
> 0.495773346159491, 0.482784058725618,
> 0.473031502762785, 0.462940836756943,
> 0.455472910452526, 0.457374752189383,
> 0.468449683385787, 0.469177346159405,
> 0.47981744053419, 0.500517935694715,
> 0.521161553352487, 0.538278248678118,
> 0.545834896270532, 0.703482475602795,
> 0.707475643569319, 0.695699528962731,
> 0.695460540915422, 0.705063229294573,
> 0.694190083263775, 0.676451221936696,
> 0.661139999162065, 0.627150885842318,
> 0.592467979293877, 0.556197511727567,
> 0.524883713023224, 0.484571801496662,
> 0.427784904562, 0.370137413134906,
> 0.331233866457343, 0.292181528642806,
> 0.265504971226103, 0.239129968439056,
> 0.21258454640671, 0.184521419432522,
> 0.160633576032345, 0.135729972994914,
> 0.115111431576686, 0.0933784744252792,
> 0.0672765522562478, 0.0397992726679255,
> 0.0118179662548541, NA, NA, NA, NA,
> 0.703482475602795, 0.70791132542366,
> 0.696508162877812, 0.672357035115831,
> 0.679831378223931, 0.702075998432084,
> 0.736057349706643, 0.759252979404642,
> 0.739391321260192, 0.706608353324493,
> 0.653481111693474, 0.607986236497692,
> 0.600942686427268, 0.602450590412635,
> 0.594096281507138, 0.598414292518021,
> 0.570859444977738, 0.50462737404968,
> 0.441225469913529, 0.37010584373766,
> 0.299554326292306, 0.250957120974181,
> 0.231147047662909, 0.218081437060998,
> 0.209354124252359, 0.212236940966109,
> 0.213898409405384, 0.200693009702681,
> 0.189880443626695, 0.175663436717225,
> 0.160910269517771, 0.14423774751828,
> 0.703482475602795, 0.707648742091919,
> 0.696092540716741, 0.656540853310246,
> 0.6051367218461, 0.591695064299013,
> 0.596015810648035, 0.603800534715597,
> 0.630728546677123, 0.658732672149451,
> 0.660216960664134, 0.675188962779905,
> 0.680940355728037, 0.677371529164165,
> 0.678862966955137, 0.706307948099043,
> 0.72103331978575, 0.71201796002067,
> 0.695266699409018, 0.685297231486624,
> 0.661576951062559, 0.643301885602357,
> 0.619830526453808, 0.608129873046412,
> 0.594283830084397, 0.562317115717112,
> 0.530350595536459, 0.506782526041746,
> 0.485311767855001, 0.473335687828819,
> 0.47767850215973, 0.47780651839627,
> 0.703482475602795, 0.708970958906805,
> 0.697551150784402, 0.661080016538957,
> 0.61232038566617, 0.587787379274781,
> 0.593431699246192, 0.585207322444761,
> 0.568559116457046, 0.548048255621954,
> 0.530114701694855, 0.534118004338362,
> 0.551070523651917, 0.575923824458594,
> 0.601811119913484, 0.599679943614892,
> 0.571040665848032, 0.537593347467274,
> 0.517448133546794, 0.509401266935977,
> 0.506839184709813, 0.513795796376072,
> 0.538416419444161, 0.54431580354862,
> 0.533416582151419, 0.536830327067308,
> 0.536462655629334, 0.513629165635279,
> 0.478995218355945, 0.438690505845544,
> 0.382567436102273, 0.34023179757446,
> 0.703482475602795, 0.708469004078862,
> 0.697978508894162, 0.676172179276398,
> 0.653999136795877, 0.621901773418305,
> 0.611086726778221, 0.593857278888487,
> 0.59772372401201, 0.615523307201519,
> 0.639972290824288, 0.642201950188424,
> 0.640462288885887, 0.599634050862654,
> 0.556922658075191, 0.51984992524725,
> 0.500551878868105, 0.481116358620079,
> 0.46280476578578, 0.439079916934238,
> 0.426481043460678, 0.4046073777228,
> 0.384894885963074, 0.387418227322783,
> 0.397735327855843, 0.382421337902373,
> 0.364609477937235, 0.351141834403433,
> 0.326023299419572, 0.298998310511409,
> 0.279388702747555, 0.265729633371279,
> 0.703482475602795, 0.708084110634261,
> 0.695308105608089, 0.680512620916581,
> 0.674409687648891, 0.64479397663385,
> 0.611185461407328, 0.574633943767944,
> 0.531967082066137, 0.509238294683539,
> 0.539380037981121, 0.605934156503129,
> 0.67139250700667, 0.692111261722321,
> 0.681033453581129, 0.649259774238939,
> 0.61340010828123, 0.601868728090964,
> 0.626623248125788, 0.630474601620122,
> 0.632877115180945, 0.622655315896617,
> 0.602457206226614, 0.577755838513823,
> 0.575613491077747, 0.56693811567409,
> 0.538199408312755, 0.508731518312269,
> 0.488361667141151, 0.462965384850233,
> 0.438776128537772, 0.433205440295598,
> 0.703482475602795, 0.708955081210283,
> 0.696337276771488, 0.675657944024044,
> 0.682199731001736, 0.713302322144747,
> 0.780735831443758, 0.836330924875064,
> 0.920042864888473, 0.993749005071184,
> 1.09383447176433, 1.13919188883409,
> 1.17120759930688, 1.20149479327377,
> 1.21627978424244, 1.16585978639785,
> 1.11758399725948, 1.04238685207932,
> 0.937208207066276, 0.862384770704829,
> 0.774099878399983, 0.701556273005073,
> 0.670583202198987, 0.686968300073611,
> 0.732378201300416, 0.820191766252091,
> 0.855392362283012, 0.845365464014818,
> 0.803317719342587, 0.757849795095728,
> 0.711624608771727, 0.674398052370244), .Dim >
c(32L, 10L))
> matplot(testdataset, type = 'l', las = 1, xlab = 'x
values',
> ylab = 'y values', main = 'title - testdataset')
> library(ggplot2,RColorBrewer,reshape2)
> testdataset[ is.na(testdataset) ] <- 0
> testdataset2 <- melt(testdataset)
> ggplot(testdataset2, aes(x=Var1,y=factor(value))) +
> stat_density(aes(fill=..density..), position="identity") +
> scale_fill_gradientn(colours=brewer.pal(n=8, name="PuBuGn"))
>
> ______________________________________________
> R-help at 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.