[R-sig-eco] correlation plot in color

Mon Mar 23 11:03:55 CET 2020

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 using uclm.es> wrote:
> 
> Thanks Bede-Fazekas Ákos, 
> 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$Treat))
> 
> Error: unexpected input in "palette <- setNames(object = c(“"
> 
> What can I do?
> Best
> Manuel 
> 
> 
> -----Mensaje original-----
> De: R-sig-ecology <r-sig-ecology-bounces using r-project.org> En nombre de Bede-Fazekas Ákos
> Enviado el: lunes, 23 de marzo de 2020 6:52
> Para: r-sig-ecology using r-project.org
> Asunto: Re: [R-sig-eco] correlation plot in color
> 
> Dear Manuel,
> 
> please try this:
> palette <- setNames(object = c(“red”, “green3”, “black”, “blue”), nm =
> levels(Libro$Treat))
> chart.Correlation(Libro[,1:4], histogram = T, pch = 19, bg=
> palette[Libro$Treat])
> 
> Have a nice week,
> Ákos
> 
> 2020.03.23. 2:40 keltezéssel, Salvador SANCHEZ COLON írta:
>> 
>> Hi Manuel,
>> 
>> 
>> I am glad that you managed to plot the correlation plots. Then, as for 
>> the colour argument, bg is the argument for setting the background 
>> color, not the symbols color; the argument controlling the symbols 
>> colour in plots is color. The error you get seems to be due to the 
>> fact that your command is missing  a square bracket at the end.
>> 
>> 
>> Still, I have never used the PerformanceAnalytics package before and I 
>> just do not know how to make the chart.Correlation function to use the 
>> color argument. My guess is that it is not designed to take such argument.
>> 
>> 
>> Salvador
>> 
>> 
>> Salvador SÁNCHEZ-COLÓN
>> 
>> An independent consultant
>> 
>> Statistics, GIS, RS
>> 
>> 
>> 
>> En Dom, 22 Marzo, 2020 en 16:42, Manuel Esteban Lucas Borja 
>> <ManuelEsteban.Lucas using uclm.es> escribió:
>> Para: Salvador SANCHEZ COLON
>> Cc: bfalevlist using gmail.com; r-sig-ecology using r-project.org
>> 
>> Thanks Salvador,
>> 
>> It Works properly and I was able to do the correlation plots excluding 
>> the categorical variable as you mentioned. In relation to colours I 
>> found the following information from other websites:
>> 
>>> data(iris)
>> 
>>> pairs(iris[1:4], main = "Data(iris) -- 3 Especies", pch = 21,bg =
>> c("red", "green3", "blue")[codes(iris$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 using prodigy.net.mx>
>> *Enviado el:* domingo, 22 de marzo de 2020 19:25
>> *Para:* Manuel Esteban Lucas Borja <ManuelEsteban.Lucas using uclm.es>
>> *CC:* bfalevlist using gmail.com; r-sig-ecology using 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 using uclm.es <mailto:ManuelEsteban.Lucas using uclm.es>>
>> escribió:
>> 
>> Para: Bede-Fazekas Ákos; r-sig-ecology using r-project.org 
>> <mailto:r-sig-ecology using 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-bounces using r-project.org
>> <mailto:r-sig-ecology-bounces using r-project.org>> En nombre de 
>> Bede-Fazekas Ákos Enviado el: domingo, 22 de marzo de 2020 16:57
>> Para: r-sig-ecology using r-project.org <mailto:r-sig-ecology using r-project.org>
>> Asunto: Re: [R-sig-eco] correlation plot in color
>> 
>> Dear Manuel,
>> 
>> since neither a reproducible example or your dataset are provided, nor 
>> the details of your problem (results of sessionInfo(); the package of 
>> corrMatOrder(); the error message you got) are known by us, it is a 
>> bit hard to help you. Anyway, I guess, that your data is not in 
>> categorical
>> (factor) but in ordinal (ordered) scale. If you convert your ordoered 
>> data to numeric with as.numeric(), then Spearman and Kendall rank 
>> correlations can be used.
>> 
>> HTH,
>> Ákos Bede-Fazekas
>> Hungarian Academy of Sciences
>> 
>> 
>> 2020.03.22. 14:29 keltezéssel, Manuel Esteban Lucas Borja írta:
>>> Dear Drew,
>>> Thank you very much for your help. The thing is that when I import
>> the dataset containing categorical and numeric variables and then I 
>> want to calculate the correlation graphic, Rstudio says that it is not 
>> posible as categorical variables can not be used for correlation. So, 
>> which is the code for calculating correlation plots including a 
>> categorical variable, which will be them used for adding colours 
>> depending of the levels of this categorical factor?
>>> Thanks a lot for your advise, I really apreciate your help.
>>> Best
>>> Manuel
>>> 
>>> 
>>> 
>>> 
>>> Manuel Esteban Lucas Borja
>>> Profesor Contratado Doctor Interino / Assistant Professor 
>>> Coordinador de Relaciones Internacionales del Campus de 
>>> Albacete/Coordinator for International Relations on Albacete Campus
>>> 
>>> Universidad de Castilla-La Mancha
>>> E.T.S. Ingenieros Agrónomos y de Montes / Higher Technical School of 
>>> Agricultural and Forestry Engineering | Campus Universitario s/n | 
>>> C.P. 02071 Albacete
>>> Tfno: 967 599 200 | Ext: 2818 |
>>> 
>>> 
>>> ________________________________
>>> From: Drew Tyre <atyre2 using unl.edu <mailto:atyre2 using unl.edu>>
>>> Sent: Sunday, March 22, 2020 2:12:31 PM
>>> To: Manuel Esteban Lucas Borja <ManuelEsteban.Lucas using uclm.es
>> <mailto:ManuelEsteban.Lucas using uclm.es>>;
>>> r-sig-ecology using r-project.org <mailto:r-sig-ecology using r-project.org>
>> <r-sig-ecology using r-project.org <mailto:r-sig-ecology using r-project.org>>
>>> Subject: Re: [R-sig-eco] correlation plot in color
>>> 
>>> Manuel,
>>> 
>>> T may be getting interpreted as TRUE, not your variable name. Try
>> renaming the variable to something else and see if that helps.
>>> 
>>> --
>>> Drew Tyre
>>> 
>>> He/him/his
>>> 
>>> While I may be sending this email outside my normal office hours, I 
>>> have no expectation to receive a reply outside of yours.
>>> 
>>> School of Natural Resources
>>> University of Nebraska-Lincoln
>>> 416 Hardin Hall, East Campus
>>> 3310 Holdrege Street
>>> Lincoln, NE 68583-0974
>>> 
>>> phone: +1 402 472 4054
>>> fax: +1 402 472 2946
>>> email: atyre2 using unl.edu <mailto:atyre2 using unl.edu> 
>>> http://snr.unl.edu/tyre http://drewtyre.rbind.io
>>> 
>>> “Anything worth doing is worth doing badly.”
>>> 
>>> * G. K. Chesterton
>>> 
>>> On 3/21/20, 8:32 PM, "R-sig-ecology on behalf of Manuel Esteban
>> Lucas Borja" <r-sig-ecology-bounces using r-project.org on behalf of 
>> ManuelEsteban.Lucas using uclm.es 
>> <mailto:r-sig-ecology-bounces using r-project.org on behalf of 
>> ManuelEsteban.Lucas using uclm.es>> wrote:
>>> 
>>> Dear all,
>>> 
>>> 
>>> 
>>> First of all, I hope this email will find you well.
>>> 
>>> 
>>> 
>>> I am working with a biological dataset (please see in attachment)
>> composed by 5 variables. The columns EMF, Biodiversity, MDS1 and MDS2 
>> are numerical variables whereas T is a categorical one.
>>> 
>>> 
>>> 
>>> I would like to obtain a correlation chart showing correlation
>> coefficients, histograms and different colours for each observation 
>> following the categorical variable "T". Please see below the initial 
>> chart I got but in which observations are not classified in different 
>> colours following the categorical variable "T".
>>> 
>>> 
>>> 
>>> This is the code I used with any positive result back.
>>> 
>>> 
>>> 
>>> corrMatOrder (dataset, histogram = T, pch = 19, method= spearman, 
>>> family="CM Roman", col=c("red", "green3", "blue",
>>> "black")[code.levels(dataset$T)])
>>> 
>>> 
>>> 
>>> I work with Rstudio. Thank you very much for your time and help.
>>> 
>>> Best
>>> 
>>> 
>>> 
>>> Manuel
>>> 
>>> 
>>> _______________________________________________
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