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>
> >
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