[R-sig-eco] correlation plot in color
Bede-Fazekas Ákos
b|@|ev||@t @end|ng |rom gm@||@com
Mon Mar 23 20:03:51 CET 2020
Dear Manuel,
the warning is saying that pairs() should be called without the
histogram parameter. But the problem of black point symbols is caused by
another thing: you chose a pch that has only color (col) but has no
background/filling color (bg). Let's choose a pch value from the 21:25
interval and both pairs() and chart.Correlation() will plot symbols
filled with colors!
Best,
Ákos
2020.03.23. 19:09 keltezéssel, Manuel Esteban Lucas Borja írta:
> Dear Ákos,
> 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 using r-project.org> En nombre de Bede-Fazekas Ákos
> Enviado el: lunes, 23 de marzo de 2020 18:46
> Para: r-sig-ecology using 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,
> Ákos
>
> 2020.03.23. 17:20 keltezéssel, Manuel Esteban Lucas Borja írta:
>> Thanks Ákos,
>>
>> 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$Treat])
>> But nothing happens. I got again the correlation plot but doc values
>> are not in colour following the Treat classification
>>
>> Thanks for your time.
>> Best
>> Manuel
>>
>>
>>
>>
>> -----Mensaje original-----
>> De: R-sig-ecology <r-sig-ecology-bounces using r-project.org> En nombre de
>> Bede-Fazekas Ákos Enviado el: lunes, 23 de marzo de 2020 14:54
>> Para: r-sig-ecology using r-project.org
>> Asunto: Re: [R-sig-eco] correlation plot in color
>>
>> Dear Manuel,
>>
>> are you sure that Libro1$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,
>> Ákos
>>
>> 2020.03.23. 11:19 keltezéssel, Manuel Esteban Lucas Borja írta:
>>> 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 using gmail.com> Enviado el: lunes, 23 de
>>> marzo de 2020 11:04
>>> Para: Manuel Esteban Lucas Borja <ManuelEsteban.Lucas using uclm.es>
>>> CC: Bede-Fazekas Ákos <bfalevlist using gmail.com>;
>>> r-sig-ecology using 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 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
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> R-sig-ecology mailing list
>>>>>> R-sig-ecology using r-project.org <mailto:R-sig-ecology using r-project.org>
>>>>>>
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