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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