[R-sig-eco] correlation plot in color

[Manuel Esteban Lucas Borja]

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> En nombre de Bede-Fazekas Ákos
Enviado el: domingo, 22 de marzo de 2020 16:57
Para: 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>
> Sent: Sunday, March 22, 2020 2:12:31 PM
> To: Manuel Esteban Lucas Borja <ManuelEsteban.Lucas using uclm.es>; 
> r-sig-ecology using r-project.org <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
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> Lincoln, NE 68583-0974
>
> phone: +1 402 472 4054
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> email: 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> 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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