Dear Ákos,
Thanks for your priceless time and help. Still not working.
> palette <- setNames(object = c("red", "green3", "black", "blue"),
> nm=levels(libro1$Treat))
Warning messages:
1: In doTryCatch(return(expr), name, parentenv, handler) :
"histogram" is not a graphical parameter
2: In doTryCatch(return(expr), name, parentenv, handler) :
"histogram" is not a graphical parameter
> pairs(libro1[,1:4], histogram = F, pch = 19, bg = palette[libro1$Treat])
There were 50 or more warnings (use warnings() to see the first 50)
And no colours on the correlation plots
Best
-----Mensaje original-----
De: R-sig-ecology <r-sig-ecology-boun...@r-project.org> En nombre de
Bede-Fazekas Ákos
Enviado el: lunes, 23 de marzo de 2020 18:46
Para: r-sig-ecology@r-project.org
Asunto: Re: [R-sig-eco] correlation plot in color
Dear Manuel,
and what happens if you use pairs() instead of chart.Correlation()? Is it
colored? If yes, then it is a possible bug in function chart.Correlation().
Best,
Ákos
2020.03.23. 17:20 keltezéssel, Manuel Esteban Lucas Borja írta:
> Thanks Ákos,
>
> I did as you mentioned:
>
>> is.factor(libro1$Treat)
> [1] FALSE
>
>> libro1$Treat <- as.factor(libro1$Treat) palette <- setNames(object =
>> c(“red”, “green3”, “black”, “blue”), nm = levels (Libro1$Treat))
>> chart.Correlation(libro1[,1:4], histogram = T, pch = 19, bg =
>> palette[Libro1$Treat])
> But nothing happens. I got again the correlation plot but doc values
> are not in colour following the Treat classification
>
> Thanks for your time.
> Best
> Manuel
>
>
>
>
> -----Mensaje original-----
> De: R-sig-ecology <r-sig-ecology-boun...@r-project.org> En nombre de
> Bede-Fazekas Ákos Enviado el: lunes, 23 de marzo de 2020 14:54
> Para: r-sig-ecology@r-project.org
> Asunto: Re: [R-sig-eco] correlation plot in color
>
> Dear Manuel,
>
> are you sure that Libro1$Treat is really a categorical column (instead of
> character)?
> The example code that you sent us works for categorical data:
> is.factor(get(data(iris))$Species)
> TRUE
> If is.factor(Libro1$Treat) is FALSE, then you should convert it from
> character to factor, before creating the color palette and calling
> chart.Correlation():
> Libro1$Treat <- as.factor(Libro1$Treat)
>
> Have a nice week,
> Ákos
>
> 2020.03.23. 11:19 keltezéssel, Manuel Esteban Lucas Borja írta:
>> Thanks Mollie,
>>
>> I have retyped all commands but nothing happens at the end. No error backs
>> and no colour in correlations plots.
>>
>>
>>> palette<-setNames(object = c("red", "green3", "black", "blue"),
>>> nm=levels(Libro1$Treat)) chart.Correlation(Libro1[,1:4],
>>> histogram=F, pch=21, bg=palette[Libro1$Treat])
>> Best
>> Manuel
>>
>>
>>
>>
>> -----Mensaje original-----
>> De: Mollie Brooks <mollieebro...@gmail.com> Enviado el: lunes, 23 de
>> marzo de 2020 11:04
>> Para: Manuel Esteban Lucas Borja <manuelesteban.lu...@uclm.es>
>> CC: Bede-Fazekas Ákos <bfalevl...@gmail.com>;
>> r-sig-ecology@r-project.org
>> Asunto: Re: [R-sig-eco] correlation plot in color
>>
>> It looks like the quotes are the fancy type (I can’t remember the official
>> word for that). Try deleting and retyping all the quotes in that command.
>>
>> cheers,
>> Mollie
>>
>>> On 23Mar 2020, at 10:52, Manuel Esteban Lucas Borja
>>> <manuelesteban.lu...@uclm.es> wrote:
>>>
>>> Thanks Bede-Fazekas Ákos,
>>> Thanks a lot for your help.
>>>
>>> I have installed also the library (colorspace) I got the following
>>> error:
>>>
>>>> palette <- setNames(object = c(“red”, “green3”, “black”, “blue”),
>>>> nm
>>>> =levels(u$Treat))
>>> Error: unexpected input in "palette <- setNames(object = c(“"
>>>
>>> What can I do?
>>> Best
>>> Manuel
>>>
>>>
>>> -----Mensaje original-----
>>> De: R-sig-ecology <r-sig-ecology-boun...@r-project.org> En nombre de
>>> Bede-Fazekas Ákos Enviado el: lunes, 23 de marzo de 2020 6:52
>>> Para: r-sig-ecology@r-project.org
>>> Asunto: Re: [R-sig-eco] correlation plot in color
>>>
>>> Dear Manuel,
>>>
>>> please try this:
>>> palette <- setNames(object = c(“red”, “green3”, “black”, “blue”), nm
>>> =
>>> levels(Libro$Treat))
>>> chart.Correlation(Libro[,1:4], histogram = T, pch = 19, bg=
>>> palette[Libro$Treat])
>>>
>>> Have a nice week,
>>> Ákos
>>>
>>> 2020.03.23. 2:40 keltezéssel, Salvador SANCHEZ COLON írta:
>>>> Hi Manuel,
>>>>
>>>>
>>>> I am glad that you managed to plot the correlation plots. Then, as
>>>> for the colour argument, bg is the argument for setting the
>>>> background color, not the symbols color; the argument controlling
>>>> the symbols colour in plots is color. The error you get seems to be
>>>> due to the fact that your command is missing a square bracket at the end.
>>>>
>>>>
>>>> Still, I have never used the PerformanceAnalytics package before
>>>> and I just do not know how to make the chart.Correlation function
>>>> to use the color argument. My guess is that it is not designed to take
>>>> such argument.
>>>>
>>>>
>>>> Salvador
>>>>
>>>>
>>>> Salvador SÁNCHEZ-COLÓN
>>>>
>>>> An independent consultant
>>>>
>>>> Statistics, GIS, RS
>>>>
>>>>
>>>>
>>>> En Dom, 22 Marzo, 2020 en 16:42, Manuel Esteban Lucas Borja
>>>> <manuelesteban.lu...@uclm.es> escribió:
>>>> Para: Salvador SANCHEZ COLON
>>>> Cc: bfalevl...@gmail.com; r-sig-ecology@r-project.org
>>>>
>>>> Thanks Salvador,
>>>>
>>>> It Works properly and I was able to do the correlation plots
>>>> excluding the categorical variable as you mentioned. In relation to
>>>> colours I found the following information from other websites:
>>>>
>>>>> data(iris)
>>>>> pairs(iris[1:4], main = "Data(iris) -- 3 Especies", pch = 21,bg =
>>>> c("red", "green3", "blue")[codes(iris$Species)])
>>>>
>>>> So the argument bg should be used for adding colours to the
>>>> correlation plot.
>>>>
>>>> bg= c(“red”, “green3”,“blue”)[codes(iris$Species)
>>>>
>>>> I tried this with my dataset:
>>>>
>>>> chart.Correlation(Libro[,1:4], histogram = T, pch = 19, bg=
>>>> c(“red”, “green3”, “black” “blue”)[codes(Libro$Treat))
>>>>
>>>> Results:
>>>>
>>>> Error: unexpected input in "chart.Correlation(u[,1:4], histogram =
>>>> T, pch = 19, bg= c(“"
>>>>
>>>>> “blue”)[codes(u$Treat))
>>>> Error: unexpected input in " “"
>>>>
>>>> Thanks a lot for your time!
>>>>
>>>> Best
>>>>
>>>> Manuel
>>>>
>>>> *De:*Salvador SANCHEZ COLON <salvadorsanchezco...@prodigy.net.mx>
>>>> *Enviado el:* domingo, 22 de marzo de 2020 19:25
>>>> *Para:* Manuel Esteban Lucas Borja <manuelesteban.lu...@uclm.es>
>>>> *CC:* bfalevl...@gmail.com; r-sig-ecology@r-project.org
>>>> *Asunto:* Re: [R-sig-eco] correlation plot in color
>>>>
>>>> Hola Manuel:
>>>>
>>>> As you have loaded the ggplot2 package, one simple way to do the
>>>> correlation plots (one at the time though) is, for example for your
>>>> pair of variables EMF and your first MSD axis:
>>>>
>>>> *ggplot*|(|data =|Libro) |+||
>>>> *geom_point*|(|mapping =||*aes*|(|x =|EMF, |y =|MSD1, |color
>>>> =|Treat))|
>>>>
>>>> I hope this helps.
>>>>
>>>> Salvador
>>>>
>>>> An independent consultant
>>>>
>>>> Biostatistics, GIS, RS
>>>>
>>>> En Dom, 22 Marzo, 2020 en 10:34, Manuel Esteban Lucas Borja
>>>> <manuelesteban.lu...@uclm.es <mailto:manuelesteban.lu...@uclm.es>>
>>>> escribió:
>>>>
>>>> Para: Bede-Fazekas Ákos; r-sig-ecology@r-project.org
>>>> <mailto:r-sig-ecology@r-project.org>
>>>>
>>>> Dear Ákos Bede-Fazekas
>>>> Sorry for the missed information. Please see the packages I used:
>>>>
>>>> library(readxl)
>>>> library(dplyr)
>>>> library(ggplot2)
>>>> library(GGally)
>>>> library(Hmisc)
>>>> library(corrplot)
>>>> library(PerformanceAnalytics)
>>>>
>>>> Then I import the attached dataset (Libro1) containing 5 variables:
>>>> EMF, bio, MSD1, MSD2 (all of them numerical) and Treat (categorical).
>>>>
>>>> Then I wrote:
>>>>
>>>>> chart.Correlation(Libro1, histogram = F, pch = 19)
>>>> And got the error:
>>>>
>>>> Error in pairs.default(x, gap = 0, lower.panel = panel.smooth,
>>>> upper.panel = panel.cor) :
>>>> non-numeric argument to 'pairs'
>>>>
>>>> And I would like to obtain the plot you can see on the doc file,
>>>> where correlation points are divided by a category (red, gren and
>>>> blue)
>>>>
>>>> Thanks a lot for your help
>>>> Manuel
>>>>
>>>>
>>>>
>>>> -----Mensaje original-----
>>>> De: R-sig-ecology <r-sig-ecology-boun...@r-project.org
>>>> <mailto:r-sig-ecology-boun...@r-project.org>> En nombre de
>>>> Bede-Fazekas Ákos Enviado el: domingo, 22 de marzo de 2020 16:57
>>>> Para: r-sig-ecology@r-project.org
>>>> <mailto:r-sig-ecology@r-project.org>
>>>> Asunto: Re: [R-sig-eco] correlation plot in color
>>>>
>>>> Dear Manuel,
>>>>
>>>> since neither a reproducible example or your dataset are provided,
>>>> nor the details of your problem (results of sessionInfo(); the
>>>> package of corrMatOrder(); the error message you got) are known by
>>>> us, it is a bit hard to help you. Anyway, I guess, that your data
>>>> is not in categorical
>>>> (factor) but in ordinal (ordered) scale. If you convert your
>>>> ordoered data to numeric with as.numeric(), then Spearman and
>>>> Kendall rank correlations can be used.
>>>>
>>>> HTH,
>>>> Ákos Bede-Fazekas
>>>> Hungarian Academy of Sciences
>>>>
>>>>
>>>> 2020.03.22. 14:29 keltezéssel, Manuel Esteban Lucas Borja írta:
>>>>> Dear Drew,
>>>>> Thank you very much for your help. The thing is that when I import
>>>> the dataset containing categorical and numeric variables and then I
>>>> want to calculate the correlation graphic, Rstudio says that it is
>>>> not posible as categorical variables can not be used for correlation.
>>>> So, which is the code for calculating correlation plots including a
>>>> categorical variable, which will be them used for adding colours
>>>> depending of the levels of this categorical factor?
>>>>> Thanks a lot for your advise, I really apreciate your help.
>>>>> Best
>>>>> Manuel
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Manuel Esteban Lucas Borja
>>>>> Profesor Contratado Doctor Interino / Assistant Professor
>>>>> Coordinador de Relaciones Internacionales del Campus de
>>>>> Albacete/Coordinator for International Relations on Albacete
>>>>> Campus
>>>>>
>>>>> Universidad de Castilla-La Mancha
>>>>> E.T.S. Ingenieros Agrónomos y de Montes / Higher Technical School
>>>>> of Agricultural and Forestry Engineering | Campus Universitario
>>>>> s/n
>>>>> | C.P. 02071 Albacete
>>>>> Tfno: 967 599 200 | Ext: 2818 |
>>>>>
>>>>>
>>>>> ________________________________
>>>>> From: Drew Tyre <aty...@unl.edu <mailto:aty...@unl.edu>>
>>>>> Sent: Sunday, March 22, 2020 2:12:31 PM
>>>>> To: Manuel Esteban Lucas Borja <manuelesteban.lu...@uclm.es
>>>> <mailto:manuelesteban.lu...@uclm.es>>;
>>>>> r-sig-ecology@r-project.org <mailto:r-sig-ecology@r-project.org>
>>>> <r-sig-ecology@r-project.org <mailto:r-sig-ecology@r-project.org>>
>>>>> Subject: Re: [R-sig-eco] correlation plot in color
>>>>>
>>>>> Manuel,
>>>>>
>>>>> T may be getting interpreted as TRUE, not your variable name. Try
>>>> renaming the variable to something else and see if that helps.
>>>>> --
>>>>> Drew Tyre
>>>>>
>>>>> He/him/his
>>>>>
>>>>> While I may be sending this email outside my normal office hours,
>>>>> I have no expectation to receive a reply outside of yours.
>>>>>
>>>>> School of Natural Resources
>>>>> University of Nebraska-Lincoln
>>>>> 416 Hardin Hall, East Campus
>>>>> 3310 Holdrege Street
>>>>> Lincoln, NE 68583-0974
>>>>>
>>>>> phone: +1 402 472 4054
>>>>> fax: +1 402 472 2946
>>>>> email: aty...@unl.edu <mailto:aty...@unl.edu>
>>>>> http://snr.unl.edu/tyre http://drewtyre.rbind.io
>>>>>
>>>>> “Anything worth doing is worth doing badly.”
>>>>>
>>>>> * G. K. Chesterton
>>>>>
>>>>> On 3/21/20, 8:32 PM, "R-sig-ecology on behalf of Manuel Esteban
>>>> Lucas Borja" <r-sig-ecology-boun...@r-project.org on behalf of
>>>> manuelesteban.lu...@uclm.es
>>>> <mailto:r-sig-ecology-boun...@r-project.org on behalf of
>>>> manuelesteban.lu...@uclm.es>> wrote:
>>>>> Dear all,
>>>>>
>>>>>
>>>>>
>>>>> First of all, I hope this email will find you well.
>>>>>
>>>>>
>>>>>
>>>>> I am working with a biological dataset (please see in attachment)
>>>> composed by 5 variables. The columns EMF, Biodiversity, MDS1 and
>>>> MDS2 are numerical variables whereas T is a categorical one.
>>>>>
>>>>> I would like to obtain a correlation chart showing correlation
>>>> coefficients, histograms and different colours for each observation
>>>> following the categorical variable "T". Please see below the
>>>> initial chart I got but in which observations are not classified in
>>>> different colours following the categorical variable "T".
>>>>>
>>>>> This is the code I used with any positive result back.
>>>>>
>>>>>
>>>>>
>>>>> corrMatOrder (dataset, histogram = T, pch = 19, method= spearman,
>>>>> family="CM Roman", col=c("red", "green3", "blue",
>>>>> "black")[code.levels(dataset$T)])
>>>>>
>>>>>
>>>>>
>>>>> I work with Rstudio. Thank you very much for your time and help.
>>>>>
>>>>> Best
>>>>>
>>>>>
>>>>>
>>>>> Manuel
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> R-sig-ecology mailing list
>>>>> R-sig-ecology@r-project.org <mailto:R-sig-ecology@r-project.org>
>>>>>
>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_
>>>>> m
>>>>> a
>>>>> il
>>>>> man_listinfo_r-2Dsig-2Decology&d=DwIFAg&c=Cu5g146wZdoqVuKpTNsYHeFX
>>>>> _
>>>>> r
>>>>> g6
>>>>> kWhlkLF8Eft-wwo&r=aLEaSryyUcERVqcKVZl7lQ&m=8ZU0mK0lLpXPq2WJfDahUzu
>>>>> 7
>>>>> C
>>>>> 12
>>>>> RW7imeOWQ_rvGsiA&s=PaGMWGrC4sn6FfrSXEvZnzrBSounwJEENXLeoXL4Cjc&e=
>>>>>
>>>>>
>>>>>
>>>>> [[alternative HTML version deleted]]
>>>>>
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