[R] Howto Superimpose Multiple Density Curves Into One Plot

Gundala Viswanath gundalav at gmail.com
Wed Sep 2 16:07:15 CEST 2009 

Thanks a million Thierry. I solved the problem
with new installation. I apologize for troubling you
in this trivial matter.

- G.V.

On Wed, Sep 2, 2009 at 10:26 PM, ONKELINX,
Thierry<Thierry.ONKELINX at inbo.be> wrote:
> I'm using the latest version: 0.8.3 on R 2.9.2
>
>
> ----------------------------------------------------------------------------
> ir. Thierry Onkelinx
> Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest
> Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance
> Gaverstraat 4
> 9500 Geraardsbergen
> Belgium
> tel. + 32 54/436 185
> Thierry.Onkelinx at inbo.be
> www.inbo.be
>
> To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of.
> ~ Sir Ronald Aylmer Fisher
>
> The plural of anecdote is not data.
> ~ Roger Brinner
>
> The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data.
> ~ John Tukey
>
> -----Oorspronkelijk bericht-----
> Van: Gundala Viswanath [mailto:gundalav at gmail.com]
> Verzonden: woensdag 2 september 2009 15:21
> Aan: ONKELINX, Thierry
> CC: r-help at stat.math.ethz.ch
> Onderwerp: Re: [R] Howto Superimpose Multiple Density Curves Into One Plot
>
> Which version of ggplot2 you use?
> Mine is:
> Version:       0.7
> Date:          2008-10-03
>
> Somehow it can't recognize facet_wrap()
>
>> ggplot(subset(dat, V2 <= 2), aes(x = V1)) + geom_density() +
>> facet_wrap(~V2)
> Error: could not find function "facet_wrap"
>>
>
> - G.V.
>
> On Wed, Sep 2, 2009 at 10:01 PM, ONKELINX, Thierry<Thierry.ONKELINX at inbo.be> wrote:
>> This code work without errors for me.
>>
>> library(ggplot2)
>> dat <- read.table("http://dpaste.com/88561/plain/")
>> ggplot(dat, aes(x = V1, colour = factor(V2))) + geom_density()
>> ggplot(dat, aes(x = V1, fill = factor(V2))) + geom_density(alpha =
>> 0.5)
>>
>> Have a look at table(dat$V2). Some classes have only 1 or 2 values,
>> which in not enough to estimate the density. Therefore you get an
>> error with
>>
>> ggplot(dat, aes(x = V1)) + geom_density() + facet_wrap(~V2)
>>
>> Subsetting the data solves the problem
>>
>> ggplot(subset(dat, V2 <= 2), aes(x = V1)) + geom_density() +
>> facet_wrap(~V2)
>>
>> HTH,
>>
>> Thierry
>>
>>
>> ----------------------------------------------------------------------
>> ------
>> ir. Thierry Onkelinx
>> Instituut voor natuur- en bosonderzoek / Research Institute for Nature
>> and Forest Cel biometrie, methodologie en kwaliteitszorg / Section
>> biometrics, methodology and quality assurance Gaverstraat 4 9500
>> Geraardsbergen Belgium tel. + 32 54/436 185 Thierry.Onkelinx at inbo.be
>> www.inbo.be
>>
>> To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of.
>> ~ Sir Ronald Aylmer Fisher
>>
>> The plural of anecdote is not data.
>> ~ Roger Brinner
>>
>> The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data.
>> ~ John Tukey
>>
>> -----Oorspronkelijk bericht-----
>> Van: Gundala Viswanath [mailto:gundalav at gmail.com]
>> Verzonden: woensdag 2 september 2009 14:54
>> Aan: ONKELINX, Thierry
>> CC: r-help at stat.math.ethz.ch
>> Onderwerp: Re: [R] Howto Superimpose Multiple Density Curves Into One
>> Plot
>>
>>> str(dat)
>> 'data.frame':   200 obs. of  2 variables:
>>  $ V1: num  0.98 0.19 1.09 0.21 0.26 0.98 0.31 0.88 0.23 0.2 ...
>>  $ V2: int  1 0 1 0 0 1 0 1 0 0 ...
>>> summary(dat)
>>       V1               V2
>>  Min.   :0.0000   Min.   :0.000
>>  1st Qu.:0.1600   1st Qu.:0.000
>>  Median :0.2950   Median :0.000
>>  Mean   :0.7108   Mean   :0.635
>>  3rd Qu.:1.0600   3rd Qu.:1.000
>>  Max.   :5.4400   Max.   :5.000
>>
>>
>> - G.V.
>>
>> On Wed, Sep 2, 2009 at 9:50 PM, ONKELINX, Thierry<Thierry.ONKELINX at inbo.be> wrote:
>>> My orginal code should work with those colnames. Note that you must not use "variable.name" but just variable.name.
>>>
>>> I guess that somethings wrong with your dataframe. What does str(dat) and summary(dat) gives?
>>>
>>> Thierry
>>>
>>>
>>> ---------------------------------------------------------------------
>>> -
>>> ------
>>> ir. Thierry Onkelinx
>>> Instituut voor natuur- en bosonderzoek / Research Institute for
>>> Nature and Forest Cel biometrie, methodologie en kwaliteitszorg /
>>> Section biometrics, methodology and quality assurance Gaverstraat 4
>>> 9500 Geraardsbergen Belgium tel. + 32 54/436 185
>>> Thierry.Onkelinx at inbo.be www.inbo.be
>>>
>>> To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of.
>>> ~ Sir Ronald Aylmer Fisher
>>>
>>> The plural of anecdote is not data.
>>> ~ Roger Brinner
>>>
>>> The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data.
>>> ~ John Tukey
>>>
>>> -----Oorspronkelijk bericht-----
>>> Van: Gundala Viswanath [mailto:gundalav at gmail.com]
>>> Verzonden: woensdag 2 september 2009 14:47
>>> Aan: ONKELINX, Thierry
>>> CC: r-help at stat.math.ethz.ch
>>> Onderwerp: Re: [R] Howto Superimpose Multiple Density Curves Into One
>>> Plot
>>>
>>> Hi Thierry,
>>>
>>> I am sorry for coming back to you.
>>> Maybe I misunderstood you, but I got this:
>>>
>>>> colnames(dat)
>>> [1] "V1" "V2"
>>>> ggplot(dat, aes(x = "V1", colour = factor("V2"))) + geom_density()
>>> Error in data.frame(..., check.names = FALSE) :
>>>  arguments imply differing number of rows: 1, 200
>>>
>>>> ggplot(dat, aes(x = V1, colour = factor(V2))) + geom_density()
>>> Error in density.default(data$x, adjust = adjust, kernel = kernel, weight = data$weight,  :
>>>  need at least 2 points to select a bandwidth automatically
>>>
>>>
>>> - G.V
>>>
>>> On Wed, Sep 2, 2009 at 9:35 PM, ONKELINX, Thierry<Thierry.ONKELINX at inbo.be> wrote:
>>>> It looks like the data has other columnnames than the samplecode you provided.
>>>>
>>>> Use colnames(dat) to get the columnnames. Replace V1 with the columnname of the values and V2 with the column name of the ID's.
>>>>
>>>> HTH,
>>>>
>>>> Thierry
>>>>
>>>>
>>>> --------------------------------------------------------------------
>>>> -
>>>> -
>>>> ------
>>>> ir. Thierry Onkelinx
>>>> Instituut voor natuur- en bosonderzoek / Research Institute for
>>>> Nature and Forest Cel biometrie, methodologie en kwaliteitszorg /
>>>> Section biometrics, methodology and quality assurance Gaverstraat 4
>>>> 9500 Geraardsbergen Belgium tel. + 32 54/436 185
>>>> Thierry.Onkelinx at inbo.be www.inbo.be
>>>>
>>>> To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of.
>>>> ~ Sir Ronald Aylmer Fisher
>>>>
>>>> The plural of anecdote is not data.
>>>> ~ Roger Brinner
>>>>
>>>> The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data.
>>>> ~ John Tukey
>>>>
>>>> -----Oorspronkelijk bericht-----
>>>> Van: Gundala Viswanath [mailto:gundalav at gmail.com]
>>>> Verzonden: woensdag 2 september 2009 14:33
>>>> Aan: ONKELINX, Thierry
>>>> CC: r-help at stat.math.ethz.ch
>>>> Onderwerp: Re: [R] Howto Superimpose Multiple Density Curves Into
>>>> One Plot
>>>>
>>>> Hi Thierry,
>>>>
>>>> Thanks for the reply. I tried this:
>>>>> dat <-   read.table("http://dpaste.com/88561/plain/")
>>>>
>>>> But I got such error:
>>>>
>>>>> ggplot(dat, aes(x = V1, colour = factor(V2))) + geom_density()
>>>> Error in density.default(data$x, adjust = adjust, kernel = kernel, weight = data$weight,  :
>>>>  need at least 2 points to select a bandwidth automatically
>>>>> ggplot(dat, aes(x = V1, fill = factor(V2))) + geom_density(alpha =
>>>>> 0.2)
>>>> Error in density.default(data$x, adjust = adjust, kernel = kernel, weight = data$weight,  :
>>>>  need at least 2 points to select a bandwidth automatically
>>>>> ggplot(dat, aes(x = V1)) + geom_density() + facet_wrap(~V2)
>>>> Error: could not find function "facet_wrap"
>>>>>
>>>>> ggplot(dat, aes(x = V1, fill = factor(V2))) + geom_density(alpha =
>>>>> 0.2)
>>>> Error in density.default(data$x, adjust = adjust, kernel = kernel, weight = data$weight,  :
>>>>  need at least 2 points to select a bandwidth automatically
>>>>> ggplot(dat, aes(x = V1)) + geom_density() + facet_wrap(~V2)
>>>> Error: could not find function "facet_wrap"
>>>>
>>>> Maybe I miss something? What could possibly go wrong?
>>>>
>>>> - Edward
>>>>
>>>>
>>>> On Wed, Sep 2, 2009 at 8:30 PM, ONKELINX, Thierry<Thierry.ONKELINX at inbo.be> wrote:
>>>>> Have a look at the ggplot2 package.
>>>>>
>>>>> library(ggplot2)
>>>>> dat <- read.table("mydat.txt")
>>>>> ggplot(dat, aes(x = V1, colour = factor(V2))) + geom_density() #or
>>>>> a few alternatives ggplot(dat, aes(x = V1, fill = factor(V2))) +
>>>>> geom_density(alpha = 0.2) ggplot(dat, aes(x = V1)) + geom_density()
>>>>> +
>>>>> facet_wrap(~V2)
>>>>>
>>>>> HTH,
>>>>>
>>>>> Thierry
>>>>>
>>>>>
>>>>> -------------------------------------------------------------------
>>>>> -
>>>>> -
>>>>> -
>>>>> --
>>>>> ----
>>>>> ir. Thierry Onkelinx
>>>>> Instituut voor natuur- en bosonderzoek / Research Institute for
>>>>> Nature and Forest Cel biometrie, methodologie en kwaliteitszorg /
>>>>> Section biometrics, methodology and quality assurance Gaverstraat 4
>>>>> 9500 Geraardsbergen Belgium tel. + 32 54/436 185
>>>>> Thierry.Onkelinx at inbo.be www.inbo.be
>>>>>
>>>>> To call in the statistician after the experiment is done may be no
>>>>> more than asking him to perform a post-mortem examination: he may
>>>>> be able to say what the experiment died of.
>>>>> ~ Sir Ronald Aylmer Fisher
>>>>>
>>>>> The plural of anecdote is not data.
>>>>> ~ Roger Brinner
>>>>>
>>>>> The combination of some data and an aching desire for an answer
>>>>> does not ensure that a reasonable answer can be extracted from a
>>>>> given body of data.
>>>>> ~ John Tukey
>>>>>
>>>>> -----Oorspronkelijk bericht-----
>>>>> Van: r-help-bounces at r-project.org
>>>>> [mailto:r-help-bounces at r-project.org]
>>>>> Namens Gundala Viswanath
>>>>> Verzonden: woensdag 2 september 2009 12:10
>>>>> Aan: r-help at stat.math.ethz.ch
>>>>> Onderwerp: [R] Howto Superimpose Multiple Density Curves Into One
>>>>> Plot
>>>>>
>>>>> I have a data that looks like this:
>>>>> http://dpaste.com/88561/plain/
>>>>>
>>>>> And I intend to create multiple density curve into one plot, where
>>>>> each curve correspond to the unique ID.
>>>>>
>>>>> I tried to use "sm" package, with this code, but without success.
>>>>>
>>>>> __BEGIN__
>>>>> library(sm)
>>>>> dat <- read.table("mydat.txt");
>>>>> plotfn <- ("~/Desktop/flowgram_superimposed.pdf");
>>>>> pdf(plotfn);
>>>>>
>>>>> sm.density.compare(dat$V1,dat$V2, xlab = "Flow Signal") colfill <-
>>>>> c(2:10); legend(locator(1), levels(dat$V2), fill=colfill)
>>>>>
>>>>> dev.off();
>>>>> __END__
>>>>>
>>>>> Please advice what's the right way to do it or if  there is
>>>>> alternative way to do it?
>>>>> I am trying to get this kind of figure:
>>>>> http://img524.imageshack.us/img524/2736/testl.png
>>>>>
>>>>>
>>>>> - G.V.
>>>>>
>>>>> ______________________________________________
>>>>> 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.
>>>>>
>>>>> Druk dit bericht a.u.b. niet onnodig af.
>>>>> Please do not print this message unnecessarily.
>>>>>
>>>>> Dit bericht en eventuele bijlagen geven enkel de visie van de
>>>>> schrijver weer en binden het INBO onder geen enkel beding, zolang
>>>>> dit bericht niet bevestigd is door een geldig ondertekend document.
>>>>> The views expressed in  this message and any annex are purely those
>>>>> of the writer and may not be regarded as stating an official
>>>>> position of INBO, as long as the message is not confirmed by a duly signed document.
>>>>>
>>>>
>>>> Druk dit bericht a.u.b. niet onnodig af.
>>>> Please do not print this message unnecessarily.
>>>>
>>>> Dit bericht en eventuele bijlagen geven enkel de visie van de
>>>> schrijver weer en binden het INBO onder geen enkel beding, zolang
>>>> dit bericht niet bevestigd is door een geldig ondertekend document.
>>>> The views expressed in  this message and any annex are purely those
>>>> of the writer and may not be regarded as stating an official
>>>> position of INBO, as long as the message is not confirmed by a duly signed document.
>>>>
>>>
>>> Druk dit bericht a.u.b. niet onnodig af.
>>> Please do not print this message unnecessarily.
>>>
>>> Dit bericht en eventuele bijlagen geven enkel de visie van de
>>> schrijver weer en binden het INBO onder geen enkel beding, zolang dit
>>> bericht niet bevestigd is door een geldig ondertekend document. The
>>> views expressed in  this message and any annex are purely those of
>>> the writer and may not be regarded as stating an official position of
>>> INBO, as long as the message is not confirmed by a duly signed document.
>>>
>>
>> Druk dit bericht a.u.b. niet onnodig af.
>> Please do not print this message unnecessarily.
>>
>> Dit bericht en eventuele bijlagen geven enkel de visie van de
>> schrijver weer en binden het INBO onder geen enkel beding, zolang dit
>> bericht niet bevestigd is door een geldig ondertekend document. The
>> views expressed in  this message and any annex are purely those of the
>> writer and may not be regarded as stating an official position of
>> INBO, as long as the message is not confirmed by a duly signed document.
>>
>
> Druk dit bericht a.u.b. niet onnodig af.
> Please do not print this message unnecessarily.
>
> Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer
> en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is
> door een geldig ondertekend document. The views expressed in  this message
> and any annex are purely those of the writer and may not be regarded as stating
> an official position of INBO, as long as the message is not confirmed by a duly
> signed document.
>

More information about the R-help mailing list