[R-sig-eco] correlation plot in color

[Bede-Fazekas Ákos]

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 <mollieebrooks using gmail.com>
> Enviado el: lunes, 23 de marzo de 2020 11:04
> Para: Manuel Esteban Lucas Borja <ManuelEsteban.Lucas using uclm.es>
> CC: Bede-Fazekas Ákos <bfalevlist using gmail.com>; r-sig-ecology using 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.Lucas using 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$Treat))
>> Error: unexpected input in "palette <- setNames(object = c(“"
>>
>> What can I do?
>> Best
>> Manuel
>>
>>
>> -----Mensaje original-----
>> De: R-sig-ecology <r-sig-ecology-bounces using r-project.org> En nombre de
>> Bede-Fazekas Ákos Enviado el: lunes, 23 de marzo de 2020 6:52
>> Para: r-sig-ecology using r-project.org
>> Asunto: Re: [R-sig-eco] correlation plot in color
>>
>> Dear Manuel,
>>
>> please try this:
>> palette <- setNames(object = c(“red”, “green3”, “black”, “blue”), nm =
>> levels(Libro$Treat))
>> chart.Correlation(Libro[,1:4], histogram = T, pch = 19, bg=
>> palette[Libro$Treat])
>>
>> Have a nice week,
>> Ákos
>>
>> 2020.03.23. 2:40 keltezéssel, Salvador SANCHEZ COLON írta:
>>> Hi Manuel,
>>>
>>>
>>> I am glad that you managed to plot the correlation plots. Then, as
>>> for the colour argument, bg is the argument for setting the
>>> background color, not the symbols color; the argument controlling the
>>> symbols colour in plots is color. The error you get seems to be due
>>> to the fact that your command is missing  a square bracket at the end.
>>>
>>>
>>> Still, I have never used the PerformanceAnalytics package before and
>>> I just do not know how to make the chart.Correlation function to use
>>> the color argument. My guess is that it is not designed to take such argument.
>>>
>>>
>>> Salvador
>>>
>>>
>>> Salvador SÁNCHEZ-COLÓN
>>>
>>> An independent consultant
>>>
>>> Statistics, GIS, RS
>>>
>>>
>>>
>>> En Dom, 22 Marzo, 2020 en 16:42, Manuel Esteban Lucas Borja
>>> <ManuelEsteban.Lucas using uclm.es> escribió:
>>> Para: Salvador SANCHEZ COLON
>>> Cc: bfalevlist using gmail.com; r-sig-ecology using r-project.org
>>>
>>> Thanks Salvador,
>>>
>>> It Works properly and I was able to do the correlation plots
>>> excluding the categorical variable as you mentioned. In relation to
>>> colours I found the following information from other websites:
>>>
>>>> data(iris)
>>>> pairs(iris[1:4], main = "Data(iris) -- 3 Especies", pch = 21,bg =
>>> c("red", "green3", "blue")[codes(iris$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 <salvadorsanchezcolon using prodigy.net.mx>
>>> *Enviado el:* domingo, 22 de marzo de 2020 19:25
>>> *Para:* Manuel Esteban Lucas Borja <ManuelEsteban.Lucas using uclm.es>
>>> *CC:* bfalevlist using gmail.com; r-sig-ecology using 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.Lucas using uclm.es <mailto:ManuelEsteban.Lucas using uclm.es>>
>>> escribió:
>>>
>>> Para: Bede-Fazekas Ákos; r-sig-ecology using r-project.org
>>> <mailto:r-sig-ecology using 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-bounces using r-project.org
>>> <mailto:r-sig-ecology-bounces using r-project.org>> En nombre de
>>> Bede-Fazekas Ákos Enviado el: domingo, 22 de marzo de 2020 16:57
>>> Para: r-sig-ecology using r-project.org
>>> <mailto:r-sig-ecology using 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 <atyre2 using unl.edu <mailto:atyre2 using unl.edu>>
>>>> Sent: Sunday, March 22, 2020 2:12:31 PM
>>>> To: Manuel Esteban Lucas Borja <ManuelEsteban.Lucas using uclm.es
>>> <mailto:ManuelEsteban.Lucas using uclm.es>>;
>>>> r-sig-ecology using r-project.org <mailto:r-sig-ecology using r-project.org>
>>> <r-sig-ecology using r-project.org <mailto:r-sig-ecology using 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: atyre2 using unl.edu <mailto:atyre2 using 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-bounces using r-project.org on behalf of
>>> ManuelEsteban.Lucas using uclm.es
>>> <mailto:r-sig-ecology-bounces using r-project.org on behalf of
>>> ManuelEsteban.Lucas using 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
>>>>
>>>>
>>>> _______________________________________________
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