correlation plot in color

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 S?NCHEZ-COL?N

An independent consultant

Statistics, GIS, RS



En Dom, 22 Marzo, 2020 en 16:42, 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

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 <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 |

<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

palette <- setNames(object = c(?red?, ?green3?, ?black?, ?blue?), nm =levels(u$Treat))

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 S?NCHEZ-COL?N

An independent consultant

Statistics, GIS, RS



En Dom, 22 Marzo, 2020 en 16:42, 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

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 <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 |

<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

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])

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 S?NCHEZ-COL?N

An independent consultant

Statistics, GIS, RS



En Dom, 22 Marzo, 2020 en 16:42, 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

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 <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 |

<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

data(iris)
pairs(iris[1:4], main = "Data(iris) -- 3 Especies", pch = 21,bg = c("red", "green3", "blue")[codes(iris$Species)])

                                                           ?blue?)[codes(u$Treat))

chart.Correlation(Libro1, histogram = F, pch = 19)

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 |

On 23Mar 2020, at 10:52, Manuel Esteban Lucas Borja <ManuelEsteban.Lucas at uclm.es> wrote:

Thanks Bede-Fazekas ?kos, 
Thanks a lot for your help. 

I have installed also the library (colorspace)
I got the following error: 

palette <- setNames(object = c(?red?, ?green3?, ?black?, ?blue?), nm =levels(u$Treat))

Error: unexpected input in "palette <- setNames(object = c(?"

What can I do?
Best
Manuel 


-----Mensaje original-----
De: R-sig-ecology <r-sig-ecology-bounces at r-project.org> En nombre de Bede-Fazekas ?kos
Enviado el: lunes, 23 de marzo de 2020 6:52
Para: r-sig-ecology at 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,
?kos

2020.03.23. 2:40 keltez?ssel, Salvador SANCHEZ COLON ?rta:

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 S?NCHEZ-COL?N

An independent consultant

Statistics, GIS, RS



En Dom, 22 Marzo, 2020 en 16:42, 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

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 <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 |

<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

	[[alternative HTML version deleted]]

palette<-setNames(object = c("red", "green3", "black", "blue"), nm=levels(Libro1$Treat))
chart.Correlation(Libro1[,1:4], histogram=F, pch=21, bg=palette[Libro1$Treat])

On 23Mar 2020, at 10:52, Manuel Esteban Lucas Borja <ManuelEsteban.Lucas at uclm.es> wrote:

Thanks Bede-Fazekas ?kos,
Thanks a lot for your help. 

I have installed also the library (colorspace) I got the following 
error:

palette <- setNames(object = c(?red?, ?green3?, ?black?, ?blue?), nm 
=levels(u$Treat))

Error: unexpected input in "palette <- setNames(object = c(?"

What can I do?
Best
Manuel


-----Mensaje original-----
De: R-sig-ecology <r-sig-ecology-bounces at r-project.org> En nombre de 
Bede-Fazekas ?kos Enviado el: lunes, 23 de marzo de 2020 6:52
Para: r-sig-ecology at 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,
?kos

2020.03.23. 2:40 keltez?ssel, Salvador SANCHEZ COLON ?rta:

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 S?NCHEZ-COL?N

An independent consultant

Statistics, GIS, RS



En Dom, 22 Marzo, 2020 en 16:42, 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

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 <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 |

<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

	[[alternative HTML version deleted]]

Thanks Mollie,

I have retyped all commands but nothing happens at the end. No error backs and no colour in correlations plots.

  

palette<-setNames(object = c("red", "green3", "black", "blue"), nm=levels(Libro1$Treat))
chart.Correlation(Libro1[,1:4], histogram=F, pch=21, bg=palette[Libro1$Treat])

Best
Manuel

  


-----Mensaje original-----
De: Mollie Brooks <mollieebrooks at gmail.com>
Enviado el: lunes, 23 de marzo de 2020 11:04
Para: Manuel Esteban Lucas Borja <ManuelEsteban.Lucas at uclm.es>
CC: Bede-Fazekas ?kos <bfalevlist at gmail.com>; r-sig-ecology at r-project.org
Asunto: Re: [R-sig-eco] correlation plot in color

It looks like the quotes are the fancy type (I can?t remember the official word for that). Try deleting and retyping all the quotes in that command.

cheers,
Mollie

On 23Mar 2020, at 10:52, Manuel Esteban Lucas Borja <ManuelEsteban.Lucas at uclm.es> wrote:

Thanks Bede-Fazekas ?kos,
Thanks a lot for your help.

I have installed also the library (colorspace) I got the following
error:

palette <- setNames(object = c(?red?, ?green3?, ?black?, ?blue?), nm
=levels(u$Treat))

Error: unexpected input in "palette <- setNames(object = c(?"

What can I do?
Best
Manuel


-----Mensaje original-----
De: R-sig-ecology <r-sig-ecology-bounces at r-project.org> En nombre de
Bede-Fazekas ?kos Enviado el: lunes, 23 de marzo de 2020 6:52
Para: r-sig-ecology at 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,
?kos

2020.03.23. 2:40 keltez?ssel, Salvador SANCHEZ COLON ?rta:

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 S?NCHEZ-COL?N

An independent consultant

Statistics, GIS, RS



En Dom, 22 Marzo, 2020 en 16:42, 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

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 <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 |

<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

	[[alternative HTML version deleted]]

is.factor(libro1$Treat) 

libro1$Treat <- as.factor(libro1$Treat)

palette <- setNames(object = c(?red?, ?green3?, ?black?, ?blue?), nm = levels (Libro1$Treat))

chart.Correlation(libro1[,1:4], histogram = T, pch = 19, bg = palette[Libro1$Treat])

Thanks Mollie,

I have retyped all commands but nothing happens at the end. No error backs and no colour in correlations plots.

  

palette<-setNames(object = c("red", "green3", "black", "blue"), 
nm=levels(Libro1$Treat)) chart.Correlation(Libro1[,1:4], histogram=F, 
pch=21, bg=palette[Libro1$Treat])

Best
Manuel

  


-----Mensaje original-----
De: Mollie Brooks <mollieebrooks at gmail.com> Enviado el: lunes, 23 de 
marzo de 2020 11:04
Para: Manuel Esteban Lucas Borja <ManuelEsteban.Lucas at uclm.es>
CC: Bede-Fazekas ?kos <bfalevlist at gmail.com>; 
r-sig-ecology at r-project.org
Asunto: Re: [R-sig-eco] correlation plot in color

It looks like the quotes are the fancy type (I can?t remember the official word for that). Try deleting and retyping all the quotes in that command.

cheers,
Mollie

On 23Mar 2020, at 10:52, Manuel Esteban Lucas Borja <ManuelEsteban.Lucas at uclm.es> wrote:

Thanks Bede-Fazekas ?kos,
Thanks a lot for your help.

I have installed also the library (colorspace) I got the following
error:

palette <- setNames(object = c(?red?, ?green3?, ?black?, ?blue?), nm
=levels(u$Treat))

Error: unexpected input in "palette <- setNames(object = c(?"

What can I do?
Best
Manuel


-----Mensaje original-----
De: R-sig-ecology <r-sig-ecology-bounces at r-project.org> En nombre de 
Bede-Fazekas ?kos Enviado el: lunes, 23 de marzo de 2020 6:52
Para: r-sig-ecology at 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,
?kos

2020.03.23. 2:40 keltez?ssel, Salvador SANCHEZ COLON ?rta:

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 S?NCHEZ-COL?N

An independent consultant

Statistics, GIS, RS



En Dom, 22 Marzo, 2020 en 16:42, 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

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 <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 |

<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

	[[alternative HTML version deleted]]

Thanks ?kos,

I did as you mentioned:

is.factor(libro1$Treat)

[1] FALSE

libro1$Treat <- as.factor(libro1$Treat)
palette <- setNames(object = c(?red?, ?green3?, ?black?, ?blue?), nm = levels (Libro1$Treat))
chart.Correlation(libro1[,1:4], histogram = T, pch = 19, bg = palette[Libro1$Treat])

But nothing happens. I got again the correlation plot but doc values are not in colour following the Treat classification

Thanks for your time.
Best
Manuel


  

-----Mensaje original-----
De: R-sig-ecology <r-sig-ecology-bounces at r-project.org> En nombre de Bede-Fazekas ?kos
Enviado el: lunes, 23 de marzo de 2020 14:54
Para: r-sig-ecology at r-project.org
Asunto: Re: [R-sig-eco] correlation plot in color

Dear Manuel,

are you sure that Libro1$Treat is really a categorical column (instead of character)?
The example code that you sent us works for categorical data:
is.factor(get(data(iris))$Species)
TRUE
If is.factor(Libro1$Treat) is FALSE, then you should convert it from character to factor, before creating the color palette and calling
chart.Correlation():
Libro1$Treat <- as.factor(Libro1$Treat)

Have a nice week,
?kos

2020.03.23. 11:19 keltez?ssel, Manuel Esteban Lucas Borja ?rta:

Thanks Mollie,

I have retyped all commands but nothing happens at the end. No error backs and no colour in correlations plots.

   

palette<-setNames(object = c("red", "green3", "black", "blue"),
nm=levels(Libro1$Treat)) chart.Correlation(Libro1[,1:4], histogram=F,
pch=21, bg=palette[Libro1$Treat])

Best
Manuel

   


-----Mensaje original-----
De: Mollie Brooks <mollieebrooks at gmail.com> Enviado el: lunes, 23 de
marzo de 2020 11:04
Para: Manuel Esteban Lucas Borja <ManuelEsteban.Lucas at uclm.es>
CC: Bede-Fazekas ?kos <bfalevlist at gmail.com>;
r-sig-ecology at r-project.org
Asunto: Re: [R-sig-eco] correlation plot in color

It looks like the quotes are the fancy type (I can?t remember the official word for that). Try deleting and retyping all the quotes in that command.

cheers,
Mollie

On 23Mar 2020, at 10:52, Manuel Esteban Lucas Borja <ManuelEsteban.Lucas at uclm.es> wrote:

Thanks Bede-Fazekas ?kos,
Thanks a lot for your help.

I have installed also the library (colorspace) I got the following
error:

palette <- setNames(object = c(?red?, ?green3?, ?black?, ?blue?), nm
=levels(u$Treat))

Error: unexpected input in "palette <- setNames(object = c(?"

What can I do?
Best
Manuel


-----Mensaje original-----
De: R-sig-ecology <r-sig-ecology-bounces at r-project.org> En nombre de
Bede-Fazekas ?kos Enviado el: lunes, 23 de marzo de 2020 6:52
Para: r-sig-ecology at 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,
?kos

2020.03.23. 2:40 keltez?ssel, Salvador SANCHEZ COLON ?rta:

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 S?NCHEZ-COL?N

An independent consultant

Statistics, GIS, RS



En Dom, 22 Marzo, 2020 en 16:42, 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

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 <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 |

<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

	[[alternative HTML version deleted]]

palette <- setNames(object = c("red", "green3", "black", "blue"), nm=levels(libro1$Treat))

pairs(libro1[,1:4], histogram = F, pch = 19, bg = palette[libro1$Treat])

Thanks ?kos,

I did as you mentioned:

is.factor(libro1$Treat)

[1] FALSE

libro1$Treat <- as.factor(libro1$Treat) palette <- setNames(object = 
c(?red?, ?green3?, ?black?, ?blue?), nm = levels (Libro1$Treat)) 
chart.Correlation(libro1[,1:4], histogram = T, pch = 19, bg = 
palette[Libro1$Treat])

But nothing happens. I got again the correlation plot but doc values 
are not in colour following the Treat classification

Thanks for your time.
Best
Manuel


  

-----Mensaje original-----
De: R-sig-ecology <r-sig-ecology-bounces at r-project.org> En nombre de 
Bede-Fazekas ?kos Enviado el: lunes, 23 de marzo de 2020 14:54
Para: r-sig-ecology at r-project.org
Asunto: Re: [R-sig-eco] correlation plot in color

Dear Manuel,

are you sure that Libro1$Treat is really a categorical column (instead of character)?
The example code that you sent us works for categorical data:
is.factor(get(data(iris))$Species)
TRUE
If is.factor(Libro1$Treat) is FALSE, then you should convert it from 
character to factor, before creating the color palette and calling
chart.Correlation():
Libro1$Treat <- as.factor(Libro1$Treat)

Have a nice week,
?kos

2020.03.23. 11:19 keltez?ssel, Manuel Esteban Lucas Borja ?rta:

Thanks Mollie,

I have retyped all commands but nothing happens at the end. No error backs and no colour in correlations plots.

   

palette<-setNames(object = c("red", "green3", "black", "blue"),
nm=levels(Libro1$Treat)) chart.Correlation(Libro1[,1:4], 
histogram=F, pch=21, bg=palette[Libro1$Treat])

Best
Manuel

   


-----Mensaje original-----
De: Mollie Brooks <mollieebrooks at gmail.com> Enviado el: lunes, 23 de 
marzo de 2020 11:04
Para: Manuel Esteban Lucas Borja <ManuelEsteban.Lucas at uclm.es>
CC: Bede-Fazekas ?kos <bfalevlist at gmail.com>; 
r-sig-ecology at r-project.org
Asunto: Re: [R-sig-eco] correlation plot in color

It looks like the quotes are the fancy type (I can?t remember the official word for that). Try deleting and retyping all the quotes in that command.

cheers,
Mollie

On 23Mar 2020, at 10:52, Manuel Esteban Lucas Borja <ManuelEsteban.Lucas at uclm.es> wrote:

Thanks Bede-Fazekas ?kos,
Thanks a lot for your help.

I have installed also the library (colorspace) I got the following
error:

palette <- setNames(object = c(?red?, ?green3?, ?black?, ?blue?), 
nm
=levels(u$Treat))

Error: unexpected input in "palette <- setNames(object = c(?"

What can I do?
Best
Manuel


-----Mensaje original-----
De: R-sig-ecology <r-sig-ecology-bounces at r-project.org> En nombre de 
Bede-Fazekas ?kos Enviado el: lunes, 23 de marzo de 2020 6:52
Para: r-sig-ecology at 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,
?kos

2020.03.23. 2:40 keltez?ssel, Salvador SANCHEZ COLON ?rta:

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 S?NCHEZ-COL?N

An independent consultant

Statistics, GIS, RS



En Dom, 22 Marzo, 2020 en 16:42, 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

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 <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 |

<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

	[[alternative HTML version deleted]]

Dear ?kos,
Thanks for your priceless time and help. Still not working.

palette <- setNames(object = c("red", "green3", "black", "blue"), nm=levels(libro1$Treat))

Warning messages:

1: In doTryCatch(return(expr), name, parentenv, handler) :
   "histogram" is not a graphical parameter
2: In doTryCatch(return(expr), name, parentenv, handler) :
   "histogram" is not a graphical parameter

pairs(libro1[,1:4], histogram = F, pch = 19, bg = palette[libro1$Treat])

There were 50 or more warnings (use warnings() to see the first 50)

And no colours on the correlation plots

  Best





-----Mensaje original-----
De: R-sig-ecology <r-sig-ecology-bounces at r-project.org> En nombre de Bede-Fazekas ?kos
Enviado el: lunes, 23 de marzo de 2020 18:46
Para: r-sig-ecology at r-project.org
Asunto: Re: [R-sig-eco] correlation plot in color

Dear Manuel,
and what happens if you use pairs() instead of chart.Correlation()? Is it colored? If yes, then it is a possible bug in function chart.Correlation().
Best,
?kos

2020.03.23. 17:20 keltez?ssel, Manuel Esteban Lucas Borja ?rta:

Thanks ?kos,

I did as you mentioned:

is.factor(libro1$Treat)

[1] FALSE

libro1$Treat <- as.factor(libro1$Treat) palette <- setNames(object =
c(?red?, ?green3?, ?black?, ?blue?), nm = levels (Libro1$Treat))
chart.Correlation(libro1[,1:4], histogram = T, pch = 19, bg =
palette[Libro1$Treat])

But nothing happens. I got again the correlation plot but doc values
are not in colour following the Treat classification

Thanks for your time.
Best
Manuel


   

-----Mensaje original-----
De: R-sig-ecology <r-sig-ecology-bounces at r-project.org> En nombre de
Bede-Fazekas ?kos Enviado el: lunes, 23 de marzo de 2020 14:54
Para: r-sig-ecology at r-project.org
Asunto: Re: [R-sig-eco] correlation plot in color

Dear Manuel,

are you sure that Libro1$Treat is really a categorical column (instead of character)?
The example code that you sent us works for categorical data:
is.factor(get(data(iris))$Species)
TRUE
If is.factor(Libro1$Treat) is FALSE, then you should convert it from
character to factor, before creating the color palette and calling
chart.Correlation():
Libro1$Treat <- as.factor(Libro1$Treat)

Have a nice week,
?kos

2020.03.23. 11:19 keltez?ssel, Manuel Esteban Lucas Borja ?rta:

Thanks Mollie,

I have retyped all commands but nothing happens at the end. No error backs and no colour in correlations plots.

    

palette<-setNames(object = c("red", "green3", "black", "blue"),
nm=levels(Libro1$Treat)) chart.Correlation(Libro1[,1:4],
histogram=F, pch=21, bg=palette[Libro1$Treat])

Best
Manuel

    


-----Mensaje original-----
De: Mollie Brooks <mollieebrooks at gmail.com> Enviado el: lunes, 23 de
marzo de 2020 11:04
Para: Manuel Esteban Lucas Borja <ManuelEsteban.Lucas at uclm.es>
CC: Bede-Fazekas ?kos <bfalevlist at gmail.com>;
r-sig-ecology at r-project.org
Asunto: Re: [R-sig-eco] correlation plot in color

It looks like the quotes are the fancy type (I can?t remember the official word for that). Try deleting and retyping all the quotes in that command.

cheers,
Mollie

On 23Mar 2020, at 10:52, Manuel Esteban Lucas Borja <ManuelEsteban.Lucas at uclm.es> wrote:

Thanks Bede-Fazekas ?kos,
Thanks a lot for your help.

I have installed also the library (colorspace) I got the following
error:

palette <- setNames(object = c(?red?, ?green3?, ?black?, ?blue?),
nm
=levels(u$Treat))

Error: unexpected input in "palette <- setNames(object = c(?"

What can I do?
Best
Manuel


-----Mensaje original-----
De: R-sig-ecology <r-sig-ecology-bounces at r-project.org> En nombre de
Bede-Fazekas ?kos Enviado el: lunes, 23 de marzo de 2020 6:52
Para: r-sig-ecology at 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,
?kos

2020.03.23. 2:40 keltez?ssel, Salvador SANCHEZ COLON ?rta:

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 S?NCHEZ-COL?N

An independent consultant

Statistics, GIS, RS



En Dom, 22 Marzo, 2020 en 16:42, 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

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 <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 |

<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

	[[alternative HTML version deleted]]