Dear Bede-Fazekas, I changed " by ' as I wrote below and nothing happens. No error back but the plot in not in colours.
> palette <- setNames(object = c ('red', 'green3', 'black', 'blue'), nm > =levels(w$Treat)) > chart.Correlation(Libro1[,1:4], histogram = F, pch = 19, > bg=palette[Libro1$Treat]) 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_ma > > il > > man_listinfo_r-2Dsig-2Decology&d=DwIFAg&c=Cu5g146wZdoqVuKpTNsYHeFX_r > > g6 > > kWhlkLF8Eft-wwo&r=aLEaSryyUcERVqcKVZl7lQ&m=8ZU0mK0lLpXPq2WJfDahUzu7C > > 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