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
>
>
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