correlation plot in color
Ok. As for your problem with the categorical variable Treat, you just exclude it when calling the chart.Correlation function. Assuming that Treat is the fifth column in your data set, then: chart.Correlation(Libro1[,1:4], histogram = F, pch = 19) should do. However, I do not know how to make the chart.Correlation function to use another variable to map colour. Salvador Salvador S?NCHEZ-COL?N An independent consultant Statistics, GIS, RS En Dom, 22 Marzo, 2020 en 12:56, Manuel Esteban Lucas Borja <ManuelEsteban.Lucas at uclm.es> escribi?: ? Para: Salvador SANCHEZ COLON Cc: bfalevlist at gmail.com; r-sig-ecology at r-project.org Gracias Salvador, ? I tried this but the question is that I would like to obtain a composite plot containing all the correlation, histograms and point colours depending on the treat variable. Thanks for your time All the best M [Logotipo UCLM<http://www.uclm.es/comun/imgweb/firma_correo/uclm.jpg>]<http://www.uclm.es/> 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 Agr?nomos y de Montes / Higher Technical School of Agricultural and Forestry Engineering | Campus Universitario s/n | C.P. 02071 Albacete Tfno: 967 599 200<tel:+34:967599200>?|?Ext: 2818<tel:+34:2818> |?ManuelEsteban.Lucas at uclm.es<mailto:ManuelEsteban.Lucas at uclm.es> http://blog.uclm.es/manuelestebanlucas/?|?Mensaje Instant?neo<sip:ManuelEsteban.Lucas at uclm.es> ???[ORCID<http://www.uclm.es/comun/imgweb/firma_correo/orcid.jpg>]<http://orcid.org/0000-0001-6270-8408>? ?[Google Scholar<http://www.uclm.es/comun/imgweb/firma_correo/googlescholar.png>]<https://scholar.google.es/citations?user=VjvdjnQAAAAJ&hl=es> [In<http://www.uclm.es/comun/imgweb/firma_correo/in.jpg>]<https://www.linkedin.com/company/uclm>? [Twitter<http://www.uclm.es/comun/imgweb/firma_correo/twitter.jpg>]<https://twitter.com/#!/uclm_es>? [Facebook<http://www.uclm.es/comun/imgweb/firma_correo/facebook.jpg>]<https://www.facebook.com/uclm.es>? [YouTube<http://www.uclm.es/comun/imgweb/firma_correo/youtube.png>]<https://www.youtube.com/user/UCLMvideos> ? Por favor, no imprima este documento si no es estrictamente necesario. Cuidar el medioambiente es responsabilidad de todos. Este mensaje de correo electr?nico puede contener informaci?n confidencial de la UCLM, siendo para uso exclusivo del destinatario. Si usted lo ha recibido por error y no es el destinatario del mensaje, le rogamos que no difunda su contenido y lo comunique al remitente. ? Please do not print this document unless absolutely necessary. Environmental protection is in our hands. This e-mail may contain confidential information of the UCLM and is exclusively intended for the addressee. If you have received it by mistake and are not the intended recipient, do not send the contents and please notify the sender. ? De: Salvador SANCHEZ COLON <salvadorsanchezcolon at prodigy.net.mx> Enviado el: domingo, 22 de marzo de 2020 19:25 Para: Manuel Esteban Lucas Borja <ManuelEsteban.Lucas at uclm.es> CC: bfalevlist at gmail.com; r-sig-ecology at 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 at uclm.es<mailto:ManuelEsteban.Lucas at uclm.es>> escribi?: ? Para: Bede-Fazekas ?kos; r-sig-ecology at r-project.org<mailto:r-sig-ecology at r-project.org> Dear ?kos 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 at r-project.org<mailto:r-sig-ecology-bounces at r-project.org>> En nombre de Bede-Fazekas ?kos Enviado el: domingo, 22 de marzo de 2020 16:57 Para: r-sig-ecology at r-project.org<mailto:r-sig-ecology at 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, ?kos Bede-Fazekas Hungarian Academy of Sciences 2020.03.22. 14:29 keltez?ssel, Manuel Esteban Lucas Borja ?rta:
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 Agr?nomos 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 at unl.edu<mailto:atyre2 at unl.edu>> Sent: Sunday, March 22, 2020 2:12:31 PM To: Manuel Esteban Lucas Borja <ManuelEsteban.Lucas at uclm.es<mailto:ManuelEsteban.Lucas at uclm.es>>; r-sig-ecology at r-project.org<mailto:r-sig-ecology at r-project.org> <r-sig-ecology at r-project.org<mailto:r-sig-ecology at 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 at unl.edu<mailto:atyre2 at 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 at r-project.org on behalf of ManuelEsteban.Lucas at uclm.es<mailto:r-sig-ecology-bounces at r-project.org on behalf of ManuelEsteban.Lucas at 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 at r-project.org<mailto:R-sig-ecology at r-project.org> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mail man_listinfo_r-2Dsig-2Decology&d=DwIFAg&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6 kWhlkLF8Eft-wwo&r=aLEaSryyUcERVqcKVZl7lQ&m=8ZU0mK0lLpXPq2WJfDahUzu7C12 RW7imeOWQ_rvGsiA&s=PaGMWGrC4sn6FfrSXEvZnzrBSounwJEENXLeoXL4Cjc&e= [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list R-sig-ecology at r-project.org<mailto:R-sig-ecology at r-project.org> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
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