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=8ZU0mK0lLpXPq2WJfDahUzu7 >>>> C >>>> 12 >>>> RW7imeOWQ_rvGsiA&s=PaGMWGrC4sn6FfrSXEvZnzrBSounwJEENXLeoXL4Cjc&e= >>>> >>>> >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> R-sig-ecology mailing list >>>> R-sig-ecology@r-project.org <mailto:R-sig-ecology@r-project.org> >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology >>> _______________________________________________ >>> R-sig-ecology mailing list >>> R-sig-ecology@r-project.org <mailto:R-sig-ecology@r-project.org> >>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology >>> _______________________________________________ R-sig-ecology >>> mailing list R-sig-ecology@r-project.org >>> <mailto:R-sig-ecology@r-project.org> >>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology >>> <https://stat.ethz.ch/mailman/listinfo/r-sig-ecology> >>> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> R-sig-ecology mailing list >> R-sig-ecology@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology >> _______________________________________________ >> R-sig-ecology mailing list >> R-sig-ecology@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology