Re: [R] need help with pdf-plot
I still have this problem. Does anybody know any solution?
Antje
Antje schrieb:
> Hello,
>
> I'm trying to plot a set of barplots like a matrix (2 rows, 10 columns
> from"reduced_mat") to a pdf. It works with the following parameters:
>
> pdf("test.pdf",width=ncol(reduced_mat)*2, height=nrow(reduced_mat)*2,
> pointsize
> = 12)
>
> par(mfcol = c(nrow(reduced_mat),ncol(reduced_mat)), oma = c(0,0,0,0),
> lwd=48/96, cex.axis = 0.5, las = 2, cex.main = 1.0)
>
> The I get a long narrow page format with the quadratic barplots.
>
> But I would like to have a A4 format in the end and the plots not filling the
> whole page (they should stay somehow quadratic and not be stretched...).
>
> What shall I look for to achieve this?
>
> Antje
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
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Re: [R] need help with pdf-plot
Thank you both!
The hint with the pty="s" was very useful. I did not know it before.
Ciao,
Antje
Ivar Herfindal schrieb:
> Dear Antje
>
> I cannot see that you have got any replies yet, so I will make and
> attempt. However, I am sure other have more formally correct solutions.
>
> When you call the pdf(), you can set paper="a4" (or "a4r" for
> landscape). However, the width and the height of your plot should then
> not exceed the size of the paper (which is approximately 8.27*11.69
> inches for "a4"). Try (I have only tested on windows XP, R 2.5.0):
>
> pdf("test1.pdf", width=10, heigh=5, paper="a4r")
> par(mfrow=c(1,3), pty="s") #pty="s" gives square plotting regions
> plot(rnorm(100))
> plot(rnorm(100))
> plot(rnorm(100))
> dev.off()
>
> Hope this helps
>
> Ivar
>
>
> Antje skrev:
>> I still have this problem. Does anybody know any solution?
>>
>> Antje
>>
>> Antje schrieb:
>>
>>> Hello,
>>>
>>> I'm trying to plot a set of barplots like a matrix (2 rows, 10
>>> columns from"reduced_mat") to a pdf. It works with the following
>>> parameters:
>>>
>>> pdf("test.pdf",width=ncol(reduced_mat)*2, height=nrow(reduced_mat)*2,
>>> pointsize = 12)
>>>
>>> par(mfcol = c(nrow(reduced_mat),ncol(reduced_mat)), oma = c(0,0,0,0),
>>> lwd=48/96, cex.axis = 0.5, las = 2, cex.main = 1.0)
>>>
>>> The I get a long narrow page format with the quadratic barplots.
>>>
>>> But I would like to have a A4 format in the end and the plots not
>>> filling the whole page (they should stay somehow quadratic and not be
>>> stretched...).
>>>
>>> What shall I look for to achieve this?
>>>
>>> Antje
>>>
>>> __
>>> R-help@stat.math.ethz.ch mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
>>> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>>
>>
>> __
>> R-help@stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
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[R] figure-definition and heatmap question
Hello,
I have two questions. I'd like to visualize data with a heatmap and I have the
following testcase:
x <- rnorm(256)
nx <- x + abs(min(x))
nnx <- 255/max(nx) * nx
x <- matrix(nnx, 16, 16)
rownames(x) <-
c("A","B","C","D","E","F","G","I","H","J","K","L","M","N","O","P")
par(fin=c(8.0,8.0))
cp <- colorRampPalette(c("white","springgreen","darkgreen"),space="Lab")
heatmap(x, Rowv = NA, Colv = NA, scale="none", col=cp(200))
I defined the figure region to make sure that each position is a square. But
with these settings I get the following output (though it looks nice):
> x <- rnorm(256)
> nx <- x + abs(min(x))
> nnx <- 255/max(nx) * nx
> x <- matrix(nnx, 16, 16)
> rownames(x) <-
c("A","B","C","D","E","F","G","I","H","J","K","L","M","N","O","P")
> par(fin=c(8.0,8.0))
> cp <- colorRampPalette(c("white","springgreen","darkgreen"),space="Lab")
> heatmap(x, Rowv = NA, Colv = NA, scale="none", col=cp(200))
Fehler in par(op) : ungültiger Wert für den Grafikparameter "fig"
spezifiziert
> par(fin=c(8.0,8.0))
> cp <- colorRampPalette(c("white","springgreen","darkgreen"),space="Lab")
> heatmap(x, Rowv = NA, Colv = NA, scale="none", col=cp(200))
Fehler in par(op) : ungültiger Wert für den Grafikparameter "fig"
spezifiziert
> par()$fig
[1] 7.267443e-04 1.305448e-02 -2.862294e-17 9.876543e-01
> par()$fin
[1] 0.08834875 7.06790021
Why do I get this error? Why does the parameters have these strange values
(though I set the fin parameter before...)
And another question concerning the heatmap: May I force the funtion to plot A1
at the upper left corner instead of the lower left?
I'll be glad about any idea how to solve these problems...
Ciao,
Antje
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Re: [R] figure-definition and heatmap question
There is no one who could help me with this?
Antje schrieb:
> Hello,
>
> I have two questions. I'd like to visualize data with a heatmap and I have
> the
> following testcase:
>
> x <- rnorm(256)
> nx <- x + abs(min(x))
> nnx <- 255/max(nx) * nx
> x <- matrix(nnx, 16, 16)
> rownames(x) <-
> c("A","B","C","D","E","F","G","I","H","J","K","L","M","N","O","P")
> par(fin=c(8.0,8.0))
> cp <- colorRampPalette(c("white","springgreen","darkgreen"),space="Lab")
> heatmap(x, Rowv = NA, Colv = NA, scale="none", col=cp(200))
>
> I defined the figure region to make sure that each position is a square. But
> with these settings I get the following output (though it looks nice):
> > x <- rnorm(256)
> > nx <- x + abs(min(x))
> > nnx <- 255/max(nx) * nx
> > x <- matrix(nnx, 16, 16)
> > rownames(x) <-
> c("A","B","C","D","E","F","G","I","H","J","K","L","M","N","O","P")
> > par(fin=c(8.0,8.0))
> > cp <- colorRampPalette(c("white","springgreen","darkgreen"),space="Lab")
> > heatmap(x, Rowv = NA, Colv = NA, scale="none", col=cp(200))
> Fehler in par(op) : ungültiger Wert für den Grafikparameter "fig"
> spezifiziert
> > par(fin=c(8.0,8.0))
> > cp <- colorRampPalette(c("white","springgreen","darkgreen"),space="Lab")
> > heatmap(x, Rowv = NA, Colv = NA, scale="none", col=cp(200))
> Fehler in par(op) : ungültiger Wert für den Grafikparameter "fig"
> spezifiziert
> > par()$fig
> [1] 7.267443e-04 1.305448e-02 -2.862294e-17 9.876543e-01
> > par()$fin
> [1] 0.08834875 7.06790021
>
> Why do I get this error? Why does the parameters have these strange values
> (though I set the fin parameter before...)
>
> And another question concerning the heatmap: May I force the funtion to plot
> A1
> at the upper left corner instead of the lower left?
>
> I'll be glad about any idea how to solve these problems...
>
> Ciao,
> Antje
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
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[R] Package installation
Hello, I'm running R with windows. Could anybody help me how to install the package biOps (http://cran.mirroring.de/src/contrib/Descriptions/biOps.html) ? I cannot find it at any mirror provided by the GUI; I just found it as "tar.gz" which cannot be installed with the installation method... Maybe, I simply do something wrong? Thanks for any hint! Antje __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] figure-definition and heatmap question
Hi Paul,
> You are getting the error because you are setting the figure region to
> be larger than the current device (typically 6 or 7 inches wide/high).
> You SHOULD be getting the error when you try par(fin), BUT there is a
> check missing in the C code, so what happens is that heatmap saves your
> par settings and then tries to reset them (this is where par(op) comes
> from), and because it saves BOTH par(fig) and par(fin) it resets both of
> them, and when it resets par(fig) there IS a check on the values, the
> values are larger than the current device and you get the error. Now,
> because there is an error in resetting par(fig), that parameter is not
> reset, so when you type par()$fin (or, equivalently, par("fin")) after
> the heatmap() call, you get the last setting that heatmap() did, which
> was from a layout inside heatmap, and so par("fig") is NOT what you set.
> Finally, there is no point in setting par(fig) before heatmap() because
> heatmap() is one of those functions that takes over the whole device
> anyway, so your par(fig), even if it was valid, would have no effect.
> If you want to make the heatmap() plot take up less of the page, you
> could set outer margins (see par(oma)), e.g., ...
>
> par(oma=rep(4, 4))
> heatmap(x, Rowv = NA, Colv = NA, scale="none", col=cp(200))
thank you very much for the explanation. Now I understand at least the strange
fig/fin values ;) There is only one question left:
> If you want to make sure that each position in the heatmap is square, DO
> NOTHING, because the layout that heatmap() sets up is using "respect" so
> the image will be square no matter what you do.
Okay, for the example, I've chosen it might be true. My initial reason to try
to force it to squares has been the visualization of matrix which is not
quadratic (e.g. 12x8). In this case heatmap stretches the coloured areas to
rectangles. I planned to set the figure region with the same length/width ratio
as the matrix is to get squares...
If I understood everything now, I have to think about something else than
heatmap to make sure to get squares, right?
Thanks, Jim, I'll test this method for my purpose :)
Ciao,
Antje
>
> Paul
>
>
>>> And another question concerning the heatmap: May I force the funtion
>>> to plot A1 at the upper left corner instead of the lower left?
>>>
>>> I'll be glad about any idea how to solve these problems...
>>>
>>> Ciao,
>>> Antje
>>>
>>> __
>>> R-help@stat.math.ethz.ch mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
>>> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>
>> __
>> R-help@stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
>
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[R] run self written functions
Hello,
I'm not sure if I'm in the right place with my question...
I'm running R on Windows and wrote a function and saved it as .R file.
It looks like this:
bmi <- function(weight, height) {
bmi <- weight / height^2
bmi
}
If I want to use this function, I have to mark everything and then press
Ctrl-R. But then everything single line is executed on the command line,
which means that I will "loose" my history when the code becomes longer.
Further, I wonder if there is any way to do some output for control
within the function (or any other possibilities to debug in a way).
Maybe, I have chosen a completely wrong way? I only want to make it easy
to create some graphical visualizations of data which will be read in by
csv. files, has to be converted and then displayed depending on some
"displaying parameters".
Ciao,
Antje
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[R] two density curves in one plot?
Hello, I was wondering if I can plot two curves I get from "density(data)" into one plot. I want to compare both. With the following commad, I just get one curve plotted: plot( density(mydata) ) Sorry for this stupid question but I could not find a solution until now... Antje __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] two density curves in one plot?
Thank you both very much. It works! __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] choose.dir
Hi all, I have written a R-script under Windows using choose.dir. Now, I have seen that this function is missing at MacOS. Does anybody know an alternative? Antje __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] choose.dir
Thank you. For Windows it works, I'll check whether it also works for Mac :) Gabor Grothendieck schrieb: > I don't have a Mac but perhaps this works: > > library(tcltk) > tclvalue(tkchooseDirectory()) > > On 5/2/07, Antje <[EMAIL PROTECTED]> wrote: >> Hi all, >> >> I have written a R-script under Windows using choose.dir. Now, I have >> seen that this function is missing at MacOS. Does anybody know an >> alternative? >> >> Antje >> >> __ >> R-help@stat.math.ethz.ch mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. >> > __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Using ComputerModern-Fonts with Matplot
Hi There, I am trying to use ComputerModern Fonts with the matplot-command. Is that possible and what command do I have to use? Thanks, Antje __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] choose.dir
Hi all, I have written a R-script under Windows using choose.dir. Now, I have seen that this function is missing at MacOS. Does anybody know an alternative? Antje __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Readline - wait for user input
Hello,
I also have problems to get to run the following lines. If I run the
block instead of every single line, it simply does not wait for the input.
Can anybody help me?
pos_name <- readline("Please type: ")
r <- substr(pos_name, 1,1)
c <- substr(pos_name, 2,nchar(pos_name))
----
Thank you!
Antje
Peter Dalgaard schrieb:
> Forest Floor wrote:
>> Hi,
>>
>> I've seen various posts on this question, but still can't get the code
>> right.
>>
>> If I run the following code one line at a time, it works fine. If I run
>> it together as a block, however, it doesn't wait for the input and gives
>> an error.
>>
>> There must be a way to have are pause/wait for an answer, but I can't
>> seem to find it. Thanks! J
>>
>> Code:
>>
>> choosefunction <- function(){readline("1. linear, 2. linear with lag, 3.
>> nonlinear ")}
>> ans <- as.integer(choosefunction())
>> if (ans==1){K2=x1}
>> if (ans==2){K2=x2 }
>> if (ans==3){K2=x3 }
>> ans
>>
>> Error text:
>> > ans <- as.integer(choosefunction())
>> 1. linear, 2. linear with lag, 3. nonlinear if (ans==1) {K2=x1}]}
>> Warning message:
>> NAs introduced by coercion
>> > if (ans==2){K2=x2) }
>> Error in if (ans == 2) { : missing value where TRUE/FALSE needed
>> > if (ans==3){K2=x3}
>> Error in if (ans == 3) { : missing value where TRUE/FALSE needed
>> > ans
>> [1] NA
>>
> As you may have realized already, the issue is that choosefunction()
> takes the next command as its input. Since "if (ans==1){K2=x1}" isn't an
> integer "ans" becomes NA, and it just goes downhill from there.
>
> An extra set of braces may help
>
>> choosefunction <- function(){readline("1. linear, 2. linear with lag, 3.
> + nonlinear ")}
>> {ans <- as.integer(choosefunction())
> + if (ans==1){K2=x1}
> + if (ans==2){K2=x2 }
> + if (ans==3){K2=x3 }
> + ans}
> 1. linear, 2. linear with lag, 3.
> nonlinear 3
> Error: object "x3" not found
>
> It still doesn't quite work, but the reason(s) for that should be plain
> to see.
>
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Readline
Hello,
I also have problems to get to run the following lines. If I run the
block instead of every single line, it simply does not wait for the input.
Can anybody help me?
pos_name <- readline("Please type: ")
r <- substr(pos_name, 1,1)
c <- substr(pos_name, 2,nchar(pos_name))
----
Thank you!
Antje
Peter Dalgaard schrieb:
> > Forest Floor wrote:
>> >> Hi,
>> >>
>> >> I've seen various posts on this question, but still can't get the
code
>> >> right.
>> >>
>> >> If I run the following code one line at a time, it works fine.
If I run
>> >> it together as a block, however, it doesn't wait for the input
and gives
>> >> an error.
>> >>
>> >> There must be a way to have are pause/wait for an answer, but I
can't
>> >> seem to find it. Thanks! J
>> >>
>> >> Code:
>> >>
>> >> choosefunction <- function(){readline("1. linear, 2. linear with
lag, 3.
>> >> nonlinear ")}
>> >> ans <- as.integer(choosefunction())
>> >> if (ans==1){K2=x1}
>> >> if (ans==2){K2=x2 }
>> >> if (ans==3){K2=x3 }
>> >> ans
>> >>
>> >> Error text:
>> >> > ans <- as.integer(choosefunction())
>> >> 1. linear, 2. linear with lag, 3. nonlinear if (ans==1) {K2=x1}]}
>> >> Warning message:
>> >> NAs introduced by coercion
>> >> > if (ans==2){K2=x2) }
>> >> Error in if (ans == 2) { : missing value where TRUE/FALSE needed
>> >> > if (ans==3){K2=x3}
>> >> Error in if (ans == 3) { : missing value where TRUE/FALSE needed
>> >> > ans
>> >> [1] NA
>> >>
> > As you may have realized already, the issue is that choosefunction()
> > takes the next command as its input. Since "if (ans==1){K2=x1}"
isn't an
> > integer "ans" becomes NA, and it just goes downhill from there.
> >
> > An extra set of braces may help
> >
>> >> choosefunction <- function(){readline("1. linear, 2. linear with
lag, 3.
> > + nonlinear ")}
>> >> {ans <- as.integer(choosefunction())
> > + if (ans==1){K2=x1}
> > + if (ans==2){K2=x2 }
> > + if (ans==3){K2=x3 }
> > + ans}
> > 1. linear, 2. linear with lag, 3.
> > nonlinear 3
> > Error: object "x3" not found
> >
> > It still doesn't quite work, but the reason(s) for that should be plain
> > to see.
> >
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[R] how to combine data of several csv-files
Hello, I'm looking for a solution for the following problem: 1) I have a folder with several csv files; each contains a set of measurement values 2) The measurements of each file belong to a position in a two dimensional matrix (lets say "B02.csv" belongs to position 2,2 3) The size of the matrix is fix 4) I cannot assure to have a csv file for each position 5) Each position belongs to one category; This information is available in a file (means 2,2 and 2,3 may belong to category "c1"; 3,2 and 3,3 may belong to category "c2") Now, I process each available file and get a vector of 6 values or NA back. The aim is to calculate mean and sd for vectors (element wise) coming from the same category (means if vec1 <- c(1,2,3,4,5,6) and vec2 <- c(6,7,8,9,10,11) belong to the same category, I would like to get mean <- c(3.5, 4.5, 5.5, 6.5, 7.5, 8.5)) ... but I'm not sure how to proceed. I end up with a list containing these vectors for each processed file and I don't know how to combine them easily... Does anybody have a suggestion for me? What I've got so far: folder <- choose.dir(getwd(), "Choose folder containing csv files") setwd(folder) rowString <- LETTERS[1:8]; cols <- 12 mat <- outer(rowString, formatC(seq(2,length=cols), flag = "0", width = 2), paste, sep = "") mat <- paste(mat, ".csv", sep = "_") layoutfilename <- file.choose() layoutfile <- read.csv(layoutfilename, sep=";", header=F, na.strings = "") classmatrix <- sapply(layoutfile,as.character) classes <- factor(classmatrix) colnames(classmatrix) <- c(1:cols) rownames(classmatrix) <- rowString ret <- sapply(mat, calcHist) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to combine data of several csv-files
Hello, sorry for this confusion but I don't know a better way to explain... I have no problems to read in the files and to process them. I end up with a list of results like this: > ret $A02.csv [1] NA $B02.csv [1] 89.130435 8.695652 2.173913 0.00 0.00 0.00 9.892473 $C02.csv [1] 86.842105 10.526316 2.631579 0.00 0.00 0.00 10.026385 $D02.csv [1] 85.00 10.00 5.00 0.00 0.00 0.00 4.474273 $E02.csv [1] 70.786517 13.483146 7.865169 5.617978 2.247191 0.00 12.125341 $F02.csv [1] 70.8 14.16667 10.0 2.5 2.5 0.0 17.26619 $G02.csv [1] 64.772727 13.636364 7.954545 11.363636 2.272727 0.00 12.735166 $H02.csv [1] NA $A03.csv [1] NA and I have a matrix with categories like this: > classmatrix 1 2 A NA NA B NA "cat1" C NA "cat1" D NA "cat1" E NA "cat2" F NA "cat2" G NA "cat2" H NA NA Now, I'm looking for a way to calculate the mean element wise for all results coming from the same category: in this case the mean of the elements: $B02.csv $C02.csv $D02.csv (belonging to "cat1") I just don't know, how to combine the result list with the categories... Does it become clearer? Probably, I try to provide a simple example but this will take some time to prepare... Thanks anyway! Antje 8rino-Luca Pantani schrieb: > I'm unclear to what it is your problem. > Import files into data frame? > Combine them in one dataframe? > Some (written) examples of the files would help people to help you out. > > An example on how to get help better and faster > >>>>>>>>>>>> > I have several csv files in the following form > V1 V2 > 1 4 > 0.3 56 > > V1 V2 > 2.5 25 > 4.5 45 > . > > I would like to import them in only one dataframe, and then recode a > column in order to get > V1 V2 V3 > 1 4 file1 > 0.3 56 file1 > 2.5 25 file2 > 4.5 45 file2 > . > >>>>>>>>>>>> > Antje ha scritto: >> Hello, >> >> I'm looking for a solution for the following problem: >> >> 1) I have a folder with several csv files; each contains a set of >> measurement values >> > __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to combine data of several csv-files
okay, I played a bit around and now I have some kind of testcase for you: v1 <- NA v2 <- rnorm(6) v3 <- rnorm(6) v4 <- rnorm(6) v5 <- rnorm(6) v6 <- rnorm(6) v7 <- rnorm(6) v8 <- rnorm(6) v8 <- NA list <- list(v1,v2,v3,v4,v5,v6,v7,v8) categ <- c(NA,"cat1","cat1","cat1","cat2","cat2","cat2",NA) > list [[1]] [1] NA [[2]] [1] -0.6442149 -0.2047012 -1.1986041 -0.2097442 -0.7343465 -1.3888750 [[3]] [1] 0.02354036 -1.36186952 -0.42197792 1.50445971 -1.76763996 0.53722404 [[4]] [1] -1.40362589 0.13045724 -0.84651458 1.57005071 0.06961015 0.25269771 [[5]] [1] -1.1829260 2.1411553 -0.1327081 -0.1053442 -0.8179396 -1.2342698 [[6]] [1] 1.17099178 0.49248118 -0.18690065 1.50050976 -0.65552410 -0.01243247 [[7]] [1] -0.046778203 -0.233788840 0.443908897 -1.649740180 0.003991354 -0.228020092 [[8]] [1] NA now, I need the means (and sd) of element 1 of list[2],list[3],list[4] (because they belong to "cat1") and = mean(-0.6442149, 0.02354036, -1.40362589) the same for element 2 up to element 6 (--> I would the get a vector containing the means for "cat1") the same for the vectors belonging to "cat2". does anybody now understand what I mean? Antje __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to combine data of several csv-files
Hello,
thank you for your help. But I guess, it's still not what I want... printing
df.my gives me
df.my
v1 v2 v3 v4 v5 v6 v7 v8
1 NA -0.6442149 0.02354036 -1.40362589 -1.1829260 1.17099178 -0.046778203 NA
2 NA -0.2047012 -1.36186952 0.13045724 2.1411553 0.49248118 -0.233788840 NA
3 NA -1.1986041 -0.42197792 -0.84651458 -0.1327081 -0.18690065 0.443908897 NA
4 NA -0.2097442 1.50445971 1.57005071 -0.1053442 1.50050976 -1.649740180 NA
5 NA -0.7343465 -1.76763996 0.06961015 -0.8179396 -0.65552410 0.003991354 NA
6 NA -1.3888750 0.53722404 0.25269771 -1.2342698 -0.01243247 -0.228020092 NA
now, I have to combine like this:
v1 v2 v3 v4 v5 v6 v7
v8
NAcat1cat1cat1 cat2cat2 cat2
NA
-->
mean(df.my$v2[1],df.my$v3[1],df.my$v4[1])
mean(df.my$v2[2],df.my$v3[2],df.my$v4[2])
mean(df.my$v2[3],df.my$v3[3],df.my$v4[3])
mean(df.my$v2[4],df.my$v3[4],df.my$v4[4])
mean(df.my$v2[5],df.my$v3[5],df.my$v4[5])
mean(df.my$v2[6],df.my$v3[6],df.my$v4[6])
the same for v5, v6 and v7
further, I'm not sure how to avoid the list, because this is the result of the
processing I did before...
Ciao,
Antje
8rino-Luca Pantani schrieb:
> I hope I see.
>
> Why not try the following, and avoid lists, which I'm not still able to
> manage properly ;-)
> v1 <- NA
> v2 <- rnorm(6)
> v3 <- rnorm(6)
> v4 <- rnorm(6)
> v5 <- rnorm(6)
> v6 <- rnorm(6)
> v7 <- rnorm(6)
> v8 <- rnorm(6)
> v8 <- NA
> (df.my <- cbind.data.frame(v1, v2, v3, v4, v5, v6, v7, v8))
> (df.my2 <- reshape(df.my,
> varying=list(c("v1","v2","v3", "v4","v5","v6","v7","v8")),
> idvar="sequential",
> timevar="cat",
> direction="long"
>))
> aggregate(df.my2$v1, by=list(category=df.my2$cat), mean)
> aggregate(df.my2$v1, by=list(category=df.my2$cat), function(x){sd(x,
> na.rm = TRUE)})
>
>
> Antje ha scritto:
>> okay, I played a bit around and now I have some kind of testcase for you:
>>
>> v1 <- NA
>> v2 <- rnorm(6)
>> v3 <- rnorm(6)
>> v4 <- rnorm(6)
>> v5 <- rnorm(6)
>> v6 <- rnorm(6)
>> v7 <- rnorm(6)
>> v8 <- rnorm(6)
>> v8 <- NA
>>
>> list <- list(v1,v2,v3,v4,v5,v6,v7,v8)
>> categ <- c(NA,"cat1","cat1","cat1","cat2","cat2","cat2",NA)
>>
>> > list
>> [[1]]
>> [1] NA
>>
>> [[2]]
>> [1] -0.6442149 -0.2047012 -1.1986041 -0.2097442 -0.7343465 -1.3888750
>>
>> [[3]]
>> [1] 0.02354036 -1.36186952 -0.42197792 1.50445971 -1.76763996
>> 0.53722404
>>
>> [[4]]
>> [1] -1.40362589 0.13045724 -0.84651458 1.57005071 0.06961015
>> 0.25269771
>>
>> [[5]]
>> [1] -1.1829260 2.1411553 -0.1327081 -0.1053442 -0.8179396 -1.2342698
>>
>> [[6]]
>> [1] 1.17099178 0.49248118 -0.18690065 1.50050976 -0.65552410
>> -0.01243247
>>
>> [[7]]
>> [1] -0.046778203 -0.233788840 0.443908897 -1.649740180 0.003991354
>> -0.228020092
>>
>> [[8]]
>> [1] NA
>>
>> now, I need the means (and sd) of element 1 of list[2],list[3],list[4]
>> (because they belong to "cat1") and
>>
>> = mean(-0.6442149, 0.02354036, -1.40362589)
>>
>> the same for element 2 up to element 6 (--> I would the get a vector
>> containing the means for "cat1")
>> the same for the vectors belonging to "cat2".
>>
>> does anybody now understand what I mean?
>>
>> Antje
>>
>>
>>
>
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Re: [R] how to combine data of several csv-files
Hi Jim,
that's exactly what I'm looking for. Thank you so much. I think, I should look
for some further documentation on list handling.
Many thanks also to "[EMAIL PROTECTED]" ;) for spending time in
finding a solution...
Have a nice day!
Antje
jim holtman schrieb:
> This should do it:
>
>> v1 <- NA
>> v2 <- rnorm(6)
>> v3 <- rnorm(6)
>> v4 <- rnorm(6)
>> v5 <- rnorm(6)
>> v6 <- rnorm(6)
>> v7 <- rnorm(6)
>> v8 <- rnorm(6)
>> v8 <- NA
>>
>> list <- list(v1,v2,v3,v4,v5,v6,v7,v8)
>> categ <- c(NA,"cat1","cat1","cat1","cat2","cat2","cat2",NA)
>>
>> # create partitioned list
>> list.cat <- split(list, categ)
>> # combine each partition into a matrix
>> list.mat <- lapply(list.cat, function(x) do.call('rbind', x))
>> # now take the means of each column
>> lapply(list.mat, colMeans)
> $cat1
> [1] -0.5699080 0.3855693 1.1051809 0.2379324 0.6684713 0.3240003
>
> $cat2
> [1] 0.38160462 -0.10559496 -0.40963090 -0.09507354 0.95021406 -0.31491450
>
>
>
> On 7/30/07, Antje <[EMAIL PROTECTED]> wrote:
>> okay, I played a bit around and now I have some kind of testcase for you:
>>
>> v1 <- NA
>> v2 <- rnorm(6)
>> v3 <- rnorm(6)
>> v4 <- rnorm(6)
>> v5 <- rnorm(6)
>> v6 <- rnorm(6)
>> v7 <- rnorm(6)
>> v8 <- rnorm(6)
>> v8 <- NA
>>
>> list <- list(v1,v2,v3,v4,v5,v6,v7,v8)
>> categ <- c(NA,"cat1","cat1","cat1","cat2","cat2","cat2",NA)
>>
>> > list
>> [[1]]
>> [1] NA
>>
>> [[2]]
>> [1] -0.6442149 -0.2047012 -1.1986041 -0.2097442 -0.7343465 -1.3888750
>>
>> [[3]]
>> [1] 0.02354036 -1.36186952 -0.42197792 1.50445971 -1.76763996 0.53722404
>>
>> [[4]]
>> [1] -1.40362589 0.13045724 -0.84651458 1.57005071 0.06961015 0.25269771
>>
>> [[5]]
>> [1] -1.1829260 2.1411553 -0.1327081 -0.1053442 -0.8179396 -1.2342698
>>
>> [[6]]
>> [1] 1.17099178 0.49248118 -0.18690065 1.50050976 -0.65552410 -0.01243247
>>
>> [[7]]
>> [1] -0.046778203 -0.233788840 0.443908897 -1.649740180 0.003991354
>> -0.228020092
>>
>> [[8]]
>> [1] NA
>>
>> now, I need the means (and sd) of element 1 of list[2],list[3],list[4]
>> (because they belong to "cat1") and
>>
>> = mean(-0.6442149, 0.02354036, -1.40362589)
>>
>> the same for element 2 up to element 6 (--> I would the get a vector
>> containing the means for "cat1")
>> the same for the vectors belonging to "cat2".
>>
>> does anybody now understand what I mean?
>>
>> Antje
>>
>> __
>> R-help@stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>
__
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Re: [R] how to combine data of several csv-files
Hey,
I had the same question concerning the sd calculation and I got the following
solution:
list <- split(list, class_vec)
list <- lapply(list, function(x) do.call('rbind', x))
my.mean <- lapply(ret, FUN = function(x) {
t <- as.matrix(x)
rm <- as.matrix(apply( t, 1, FUN = function(w) { length(which(is.na(w)
==
TRUE)) } ))
t <- matrix(t[rm == 0,], ncol=7)
# I had to do the 2 lines above to remove rows belonging to a class but
containing NA values... (cannot exclude)
if(nrow(t) > 1) {
apply(t, 2, mean)
} else {
if(nrow(t) == 1) { as.vector(t) }
else { NA }
}
})
Probably, there is a simpler solution to remove the NA rows, but it works ;);
also with "sd".
Ciao,
Antje
8rino-Luca Pantani schrieb:
>> Hi Jim,
>> that's exactly what I'm looking for. Thank you so much. I think, I
>> should look for some further documentation on list handling.
> I think I will do the same...
> Thanks to Jim I learned "textConnection" and "rowMeans".
>
> Jim, could you please go a step further and tell me how to use lapply to
> calculate
> the sd instead of the mean of the same items?
> I mean
> sd(-0.6442149 0.02354036 -1.40362589)
> sd(-1.1829260 1.17099178 -0.046778203)
> sd(-0.2047012 -1.36186952 0.13045724)
> etc
>
> x <- read.table(textConnection(" v1 v2 v3 v4 v5 v6 v7 v8
> NA -0.6442149 0.02354036 -1.40362589 -1.1829260 1.17099178
> -0.046778203 NA
> NA -0.2047012 -1.36186952 0.13045724 2.1411553 0.49248118
> -0.233788840 NA
> NA -1.1986041 -0.42197792 -0.84651458 -0.1327081 -0.18690065
> 0.443908897 NA
> NA -0.2097442 1.50445971 1.57005071 -0.1053442 1.50050976
> -1.649740180 NA
> NA -0.7343465 -1.76763996 0.06961015 -0.8179396 -0.65552410
> 0.003991354 NA
> NA -1.3888750 0.53722404 0.25269771 -1.2342698 -0.01243247
> -0.228020092 NA"), header=TRUE)
>
>
>
>
>
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[R] remove NA rows and columns
Hello, I guess, it's a rather simple thing but I cannot find a short way to reduce a matrix, removing all rows and columns having just NA elements. testmatrix <- matrix(nrow=6, ncol=4) testmatrix[2:5,2:3] <- seq(2) > testmatrix [,1] [,2] [,3] [,4] [1,] NA NA NA NA [2,] NA11 NA [3,] NA22 NA [4,] NA11 NA [5,] NA22 NA [6,] NA NA NA NA the new matrix should look like this (by the way, I don't "know" which rows and columns are the one to be deleted... > testmatrix [,1] [,2] [1,] 11 [2,] 22 [3,] 11 [4,] 22 Ciao, Antje __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] remove NA rows and columns
Hello, thank you both very much! It is as easy as expected... (I think I still have to learn a lot!) Have a nice day! Antje Vladimir Eremeev schrieb: > Or, these operations can be called in one command: > >> testmatrix[-which(apply(testmatrix,1,function(x)all(is.na(x,-which(apply(testmatrix,2,function(x)all(is.na(x] > [,1] [,2] > [1,]11 > [2,]22 > [3,]11 > [4,]22 > > > > Vladimir Eremeev wrote: >>> testmatrix >> [,1] [,2] [,3] [,4] >> [1,] NA NA NA NA >> [2,] NA11 NA >> [3,] NA22 NA >> [4,] NA11 NA >> [5,] NA22 NA >> [6,] NA NA NA NA >> >>> tm1<-testmatrix[,-which(apply(testmatrix,2,function(x)all(is.na(x] >>> tm1 >> [,1] [,2] >> [1,] NA NA >> [2,]11 >> [3,]22 >> [4,]11 >> [5,]22 >> [6,] NA NA >> >>> tm2<-tm1[-which(apply(testmatrix,1,function(x)all(is.na(x,] >>> tm2 >> [,1] [,2] >> [1,]11 >> [2,]22 >> [3,]11 >> [4,]22 >> >> >> Antje wrote: >>> I guess, it's a rather simple thing but I cannot find a short way to >>> reduce a >>> matrix, removing all rows and columns having just NA elements. >>> >>> testmatrix <- matrix(nrow=6, ncol=4) >>> testmatrix[2:5,2:3] <- seq(2) >>> >>> > testmatrix >>> [,1] [,2] [,3] [,4] >>> [1,] NA NA NA NA >>> [2,] NA11 NA >>> [3,] NA22 NA >>> [4,] NA11 NA >>> [5,] NA22 NA >>> [6,] NA NA NA NA >>> >>> the new matrix should look like this (by the way, I don't "know" which >>> rows and >>> columns are the one to be deleted... >>> >>> > testmatrix >>> [,1] [,2] >>> [1,] 11 >>> [2,] 22 >>> [3,] 11 >>> [4,] 22 >>> >> > __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] need help with pdf-plot
Hello,
I'm trying to plot a set of barplots like a matrix (2 rows, 10 columns
from"reduced_mat") to a pdf. It works with the following parameters:
pdf("test.pdf",width=ncol(reduced_mat)*2, height=nrow(reduced_mat)*2, pointsize
= 12)
par(mfcol = c(nrow(reduced_mat),ncol(reduced_mat)), oma = c(0,0,0,0),
lwd=48/96, cex.axis = 0.5, las = 2, cex.main = 1.0)
The I get a long narrow page format with the quadratic barplots.
But I would like to have a A4 format in the end and the plots not filling the
whole page (they should stay somehow quadratic and not be stretched...).
What shall I look for to achieve this?
Antje
__
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[R] tapply, how to get level information
Hello,
I'm applying a self-written function to a matrix on basis of different
levels.
Is there any way, to get the level information within the self-written
function???
t <- tapply(mat, levels, plotDensity)
plotDensity <- function(x) {
??? print(level(x)) ???
}
Antje
__
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[R] Error in plot.new() : Figure margins too large
Hello,
was could be the reason for such an error message???
I'd like to create a window with 10x6 barplot and save it as pdf.
I tried:
pdf("histogram.pdf",width=7, height=7)
windows(cols, rows)
par(mfcol = c(rows,cols))
sapply(mat, calcHist)
dev.off()
Within the method of sapply, I call barplot
What is wrong???
Antje
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Re: [R] Error in plot.new() : Figure margins too large
Hmm, but what can be the solution? Any idea? Or any documentation on
that which I could read to find a solution by myself?
with the windows statement, I wanted to achive a format which fits for
my plots, so that each plot will have a quadratic area.
I guess, I did not unstand that much of windows / margins and plotting
areas. Maybe someone can help me (even with a good overview on these
basics...)
Antje
Peter Dalgaard schrieb:
> Antje wrote:
>> Hello,
>>
>> was could be the reason for such an error message???
>>
> Generically, that the (per-subplot) figure region is so small that
> subtracting margins leaves nowhere to plot. Reasons include: Plotting
> area too small, too many subplots, too many lines of text in margins,
> too large font size in margins.
>
>> I'd like to create a window with 10x6 barplot and save it as pdf.
>>
>> I tried:
>>
>> pdf("histogram.pdf",width=7, height=7)
>>
> What did you expect the following line to do? I think it doesn't...
>> windows(cols, rows)
>>
>
>
>> par(mfcol = c(rows,cols))
>>
>> sapply(mat, calcHist)
>>
>> dev.off()
>>
>> Within the method of sapply, I call barplot
>>
>> What is wrong???
>>
>> Antje
>>
>> __
>> R-help@stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] sapply and its return value
Hello,
I have some problems with sapply. I wanted to do the following:
s <- sapply(filelist, function(x) {
if(file.exists(x))
{
...
return( list(density(file$V1)$x, density(file$V1)$y))
}
else
{
print(paste("plotDensity ERROR - File does not exist:
",x,sep=""))
return( NULL)
}
})
if(is.null( - ??? - ))
{
print("no plot")
}
That means, I try to read every file and to get some data from it. It
may happen, that the file does not exist and then I don't want to plot
anything. As return, I get a list and I have quite a lot of problems to
access its content... (I did not really understand how this works, I
guess...)
Could anybody give me a hint?
Thank you!
Antje
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[R] tapply, levelinformation
Hello, I have another question. I would like to plot something within a self written function (plotdensity) called by tapply t <- tapply(mat, classes, plotdensity) Now I would like to add each plot the class/level as title. How can I do this? Antje __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] tapply, levelinformation
Hi Jim, jim holtman schrieb: > Here is one way: > > t <- split(mat, classes) > for (i in names(t)) plotdensity(t[[i]], main=i) > But then I don't use the advantages of the tapply anymore... > What is the problem you are trying to solve? I have a set of data (multiple files), which belong to different conditions (one or more files per condition). I wanted to read the data set and a "description" of the conditions and then automatically create plots for data of the same condition. Maybe it's much to complicate the way I do... Antje __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] sapply again return value
Hello, I used an sapply to get some data back (s <- sapply(...) ). The output of s would then deliver something like this: B06_lamp.csv C06_lamp.csv D06_lamp.csv [1,] NULL NULL Numeric,512 [2,] NULL NULL Numeric,512 [3,] NULL NULL 2 > mode(s) [1] "list" > dim(s) [1] 3 3 > Now, I'd like to remove the columns which contain NULL (it's alway the whole column). How can I do this??? Antje __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] sapply again return value
Henrique Dallazuanna schrieb: > Hi, > A simple way is: > > s <- s[3] but what if I don't know how many and which columns are NULL? Antje __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] variables with dynamic names?
Hello, I have the following problem. I have a set of CSV files and they are named for a special position in a matrix (e.g. "A01.csv", "F06.csv", "H11.csv") Now, I would like to read in the data of all these files and eveluate something for each set (and write it at the position in a result matrix). How can I realize this with R? Ciao, Antje __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] variables with dynamic names?
Thanks very much for your help.
I found the solution. I created a matrix with Strings and within a loop
I read the files and processed them
wellInfo <- matrix(nrow = rows, ncol = cols)
for(i in 1:rows) {
tempRow <- paste(rowString[i], formatC(c(1:cols), flag="0",
width=2), sep="")
print(tempRow)
wellInfo[i,] <- tempRow
}
for(i in 1:rows) {
for(j in 1:cols) {
filename <- paste(wellInfo[i,j],".csv",sep="")
if( file.exists(filename)) {
file <- read.csv(filename, sep="\t", header=F)
...
}
}
}
(It was quite simple, but I did not find the "paste" command before...)
If there is something which could be done easier, just let me know.
Ciao,
Antje
Antje schrieb:
> Hello,
>
> I have the following problem. I have a set of CSV files and they are
> named for a special position in a matrix (e.g. "A01.csv", "F06.csv",
> "H11.csv")
>
> Now, I would like to read in the data of all these files and eveluate
> something for each set (and write it at the position in a result matrix).
> How can I realize this with R?
>
> Ciao,
> Antje
>
> __
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>
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[R] extract values from a vector
Hello,
I'm looking for a solution for the following problem:
I have two vectors
V1 <- c("apple","honey","milk","bread","butter")
V2 <- c("bread","milk")
now, I would like to know for each element in V1 if it's equal to one of
the elements in V2
I could do:
which(V1 == V2[1] | V1 == V2[2])
but what if I don't know the length of V2 and it's content???
Thank you in advance!
Antje
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Re: [R] extract values from a vector
Bernd Weiss schrieb:
> Am 1 Nov 2006 um 14:49 hat Antje geschrieben:
>
> Date sent:Wed, 01 Nov 2006 14:49:43 +0100
> From: Antje <[EMAIL PROTECTED]>
> To: R-help@stat.math.ethz.ch
> Subject: [R] extract values from a vector
>
>
>> Hello,
>>
>> I'm looking for a solution for the following problem:
>> I have two vectors
>>
>> V1 <- c("apple","honey","milk","bread","butter")
>> V2 <- c("bread","milk")
>>
>> now, I would like to know for each element in V1 if it's equal to one
>> of the elements in V2 I could do: which(V1 == V2[1] | V1 == V2[2])
>>
>> but what if I don't know the length of V2 and it's content???
>>
>>
>
>
>> V1%in%V2
>>
> [1] FALSE FALSE TRUE TRUE FALSE
>
> Is this what you are looking for?
>
> HTH,
>
> Bernd
>
>
Thank you very much, that's what I need (I'm sorry for asking so stupid
questions)
Antje
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[R] barplot - x-axis
Hi there, I have a barplot and the labels at the x-axis are strings, which are rotated by 90°. But now the sub-title of the barplot is in between these labels, which does not look very nice... Could anybody help me finding the parameter-setting to prevent this? par(mai=c(1.5,1,1,0.6)) barplot(data, las=2, ylim = c(0,plotMax+1), ylab = "Percentage", main = filename, sub = subtitle) Thank you! Antje __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] barplot help needed
hello, I would like to create the following barplot: I have 4 different data sets (same length + stddev for each data point) data1 sd1 data2 sd2 data3 sd3 data4 sd4 now, I'd like to plot in the following way: data1[1],data2[1],data3[1],data4[1] with it's sd-values side-by-side at one x-axis label (named "position 1") and each bar in different colors. data1[2],data2[2],data3[2],data4[2] at the next x-axis label (named "position 2") with the same color scheme and so on over the whole length. I managed to plot one set in the following way: par(mai=c(1.5,1,1,0.6)) plotInfo <- barplot(data1, las=2, ylim = c(0,plotMax+1), ylab = "Percentage") arrows(plotInfo,data1,plotInfo, data1 + sd1, length=0.1, angle=90) arrows(plotInfo,data1,plotInfo, data1 - sd1, length=0.1, angle=90) could anybody give me a help on this? Antje __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] barplot help needed
Thank you very much for your help. I just don't understand the following line (which also gives me a dimension error later in the arrows command) etype <- rep(c(sd1, sd2, sd3, sd4), length(data1)) Antje (I don't see my emails to the mailinglist anymore... just the answers from other people... I don't understand???) Jacques VESLOT schrieb: > tab <- do.call(rbind, list(data1, data2, data3, data4)) > etype <- rep(c(sd1, sd2, sd3, sd4), length(data1)) > b <- barplot(tab, beside=T) > arrows(unlist(b), unlist(tab) - etype, unlist(b), unlist(tab) + etype, > code=3) > --- > Jacques VESLOT > > CNRS UMR 8090 > I.B.L (2ème étage) > 1 rue du Professeur Calmette > B.P. 245 > 59019 Lille Cedex > > Tel : 33 (0)3.20.87.10.44 > Fax : 33 (0)3.20.87.10.31 > > http://www-good.ibl.fr > --- > > Antje a écrit : >> hello, >> >> I would like to create the following barplot: >> >> I have 4 different data sets (same length + stddev for each data point) >> >> data1 >> sd1 >> data2 >> sd2 >> data3 >> sd3 >> data4 >> sd4 >> >> now, I'd like to plot in the following way: >> >> data1[1],data2[1],data3[1],data4[1] with it's sd-values side-by-side >> at one x-axis label (named "position 1") and each bar in different >> colors. >> >> data1[2],data2[2],data3[2],data4[2] at the next x-axis label (named >> "position 2") with the same color scheme >> >> and so on over the whole length. >> >> I managed to plot one set in the following way: >> >> par(mai=c(1.5,1,1,0.6)) >> plotInfo <- barplot(data1, las=2, ylim = c(0,plotMax+1), ylab = >> "Percentage") >> arrows(plotInfo,data1,plotInfo, data1 + sd1, length=0.1, angle=90) >> arrows(plotInfo,data1,plotInfo, data1 - sd1, length=0.1, angle=90) >> >> could anybody give me a help on this? >> >> Antje >> >> __ >> R-help@stat.math.ethz.ch mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. >> > __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] barplot help needed
Still, there is one problem. The SD-Values don't fit to the bar they belong to. I made the following experiment: > data1 <- c(2,4,6,2,5) > data2 <- data1 > sd1 <- c(0.5,1,1.5,1,2) > sd2 <- sd1 > tab <- do.call(rbind, list(data1, data2)) > etype <- c(sd1,sd2) > b <- barplot(tab, beside=T) > arrows(unlist(b), unlist(tab) - etype, unlist(b), unlist(tab) + etype, code=3) I expect the bars with the same height and the same stddev. The height is okay, but the stddev is messed up... if I do it like this: etype <- matrix(c(sd1,sd2), nrow=2, byrow=TRUE) it works (but maybe there is an easier way...) Antje Jacques VESLOT schrieb: > thought sd1, sd2... were scalars but if not just do: > etype <- c(sd1, sd2, sd3, sd4) > --- > Jacques VESLOT > > CNRS UMR 8090 > I.B.L (2ème étage) > 1 rue du Professeur Calmette > B.P. 245 > 59019 Lille Cedex > > Tel : 33 (0)3.20.87.10.44 > Fax : 33 (0)3.20.87.10.31 > > http://www-good.ibl.fr > --- > > > Antje a écrit : >> Thank you very much for your help. >> I just don't understand the following line (which also gives me a >> dimension error later in the arrows command) >> >> etype <- rep(c(sd1, sd2, sd3, sd4), length(data1)) >> >> Antje >> >> (I don't see my emails to the mailinglist anymore... just the answers >> from other people... I don't understand???) >> >> >> Jacques VESLOT schrieb: >> >>> tab <- do.call(rbind, list(data1, data2, data3, data4)) >>> etype <- rep(c(sd1, sd2, sd3, sd4), length(data1)) >>> b <- barplot(tab, beside=T) >>> arrows(unlist(b), unlist(tab) - etype, unlist(b), unlist(tab) + >>> etype, code=3) >>> --- >>> Jacques VESLOT >>> >>> CNRS UMR 8090 >>> I.B.L (2ème étage) >>> 1 rue du Professeur Calmette >>> B.P. 245 >>> 59019 Lille Cedex >>> >>> Tel : 33 (0)3.20.87.10.44 >>> Fax : 33 (0)3.20.87.10.31 >>> >>> http://www-good.ibl.fr >>> --- >>> >>> Antje a écrit : >>> >>>> hello, >>>> >>>> I would like to create the following barplot: >>>> >>>> I have 4 different data sets (same length + stddev for each data point) >>>> >>>> data1 >>>> sd1 >>>> data2 >>>> sd2 >>>> data3 >>>> sd3 >>>> data4 >>>> sd4 >>>> >>>> now, I'd like to plot in the following way: >>>> >>>> data1[1],data2[1],data3[1],data4[1] with it's sd-values side-by-side >>>> at one x-axis label (named "position 1") and each bar in different >>>> colors. >>>> >>>> data1[2],data2[2],data3[2],data4[2] at the next x-axis label (named >>>> "position 2") with the same color scheme >>>> >>>> and so on over the whole length. >>>> >>>> I managed to plot one set in the following way: >>>> >>>> par(mai=c(1.5,1,1,0.6)) >>>> plotInfo <- barplot(data1, las=2, ylim = c(0,plotMax+1), ylab = >>>> "Percentage") >>>> arrows(plotInfo,data1,plotInfo, data1 + sd1, length=0.1, angle=90) >>>> arrows(plotInfo,data1,plotInfo, data1 - sd1, length=0.1, angle=90) >>>> >>>> could anybody give me a help on this? >>>> >>>> Antje >>>> >>>> __ >>>> R-help@stat.math.ethz.ch mailing list >>>> https://stat.ethz.ch/mailman/listinfo/r-help >>>> PLEASE do read the posting guide >>>> http://www.R-project.org/posting-guide.html >>>> and provide commented, minimal, self-contained, reproducible code. >>>> >>> >> >> __ >> R-help@stat.math.ethz.ch mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. >> > __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Multiple plots via sapply or lapply?
Hi all,
I've got the following problem. I have a vector containing file names. I
want to read these files as csv and calculate the density-function for
each file (has just one column with data). Then, I'd like to plot all
density functions into one window. I did the following to calculate the
density data:
s <- sapply(filelist, function(x) {
if(file.exists(x))
{
file <- read.csv(x, sep="\t", header=F)
return( list(density(file$V1)$x, density(file$V1)$y))
}
})
Now I would like to plot these x,y data in a similar way but my result
"s" is a matrix containing lists...
File1.csv File2.csv File3.csv
[1,] Numeric,512Numeric,512 Numeric,512
[2,] Numeric,512Numeric,512 Numeric,512
Now I don't know how to handle the x,y values for each plot into an
sapply (or lapply, I don't know)
Any idea? Maybe, I should somehow change the return type?
Antje
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[R] How to save an object list as txt?
Hello everyone, does somebody know how can I save an object list as a txt-file or as a csv-file? The problem is, that the elements of this list have different row length. So I cannot convert the list into a matrix or something else and then use "write-matrix" or so as usual. Thank you very much for your help. Regards, Antje [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] panel order in xyplot
Hi all,
I have a question concerning xyplot. My data is a data.frame looking like that:
In the first column I have numbers from 0 to 23 (hours of a day), the second
column contains the name of a weekday (Day as factor) and the third column
contains the number I am interested in. So as an example, the first five rows
look like that:
Hour Day Freq
1 0 Mo23
2 1 Mo20
3 2 Mo14
4 3 Mo27
5 4 Mo26
To read: On Monday between 0 and 1 o'clock 23 things happened.
The code of the xyplot looks like that:
trellis.device(new = FALSE, col = FALSE)
xyplot(Freq ~ Hour | Day, data = mydata,
xlab = "hour", ylab = "number", main = "xxx", ylim = 1:30,
scales = list(x = list(at = seq(0,24,6), labels = c(0, 6, 12, 18, 24),
cex = 0.7, relation = "free"),
y = list(tick.number = 5, cex = 0.7)), between = list(x = 0.5, y = 1.5),
layout = c(4,2), aspect = 1,
panel = function(x,y){
panel.grid()
panel.barchart(x, y, horiz = F, aspect = 1, col = "red")
}
)
Now my problem:
The plot is ordered by default, that in the first row I can see Friday,
Saturday and Sunday, in the second row there is Monday, Tuesday, Wednesday and
Thursday. I like to order the panels that way that in the first row there
should be Monday-Thursday, the last row to contain Friday - Sunday.
Is there any parameter in xyplot I can add to achieve this result? Any
parameter where I can tell how the panels have to be arranged?
Thanks a lot for any help.
Antje
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[R] two y-axis in xy-plot
Hi there, I am wondering if it is possible to do an xyplot with two y-axes. I'd like to print two parameters in a time series but they both have different scales. Which parameter in xyplot can I add to achieve this result? Thanks a lot for any help. Antje [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] two y-axis in xy-plot
It is nearly the same example I wrote about in http://www.mail-archive.com/r-help@stat.math.ethz.ch/msg54238.html. I'll print it out again: In the first column I have numbers from 0 to 23 (hours of a day), the second column contains the name of a weekday (Day as factor) and the third column contains the number I am interested in. So as an example, the first five rows look like that: Hour Day Freq 1 0 Mo23 2 1 Mo20 3 2 Mo14 4 3 Mo27 5 4 Mo26 To read: On Monday between 0 and 1 o'clock 23 things happened. Now I add a new parameter, so that the data looks somehow like that: Hour Day Freq Freq2 1 0 Mo23 874 2 1 Mo20 476 3 2 Mo14 201 4 3 Mo27 912 5 4 Mo26 172 Now I'd like to have a plot for every weekday containing the two frequencies as a line during the hours. Is this possible with two y-axes? Thanks for your help, Antje -Ursprüngliche Nachricht- Von: Deepayan Sarkar [mailto:[EMAIL PROTECTED] Gesendet: Montag, 9. Januar 2006 18:08 An: Antje Schüle Cc: r-help@stat.math.ethz.ch Betreff: Re: two y-axis in xy-plot On 1/9/06, Antje Schüle <[EMAIL PROTECTED]> wrote: > Hi there, > > > > I am wondering if it is possible to do an xyplot with two y-axes. I'd like > to print two parameters in a time series but they both have different > scales. > > > > Which parameter in xyplot can I add to achieve this result? The answer depends on the details of what you are doing, so please provide us with a reproducible example. Deepayan __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] two y-axis in xy-plot
Hi all, I think there is something I have forgotten to emphasize. I'd like to have an xyplot (with lattice library). A trellis graphic. For every weekday I like to have a graphic with all hours. And inside the graphic there are the two frequencies as lines. The problem finally is the use of the xyplot in library(lattice) in combination with the second y-axis. Thanks. Antje --- It is nearly the same example I wrote about in http://www.mail-archive.com/r-help@stat.math.ethz.ch/msg54238.html. I'll print it out again: In the first column I have numbers from 0 to 23 (hours of a day), the second column contains the name of a weekday (Day as factor) and the third column contains the number I am interested in. So as an example, the first five rows look like that: Hour Day Freq 1 0 Mo23 2 1 Mo20 3 2 Mo14 4 3 Mo27 5 4 Mo26 To read: On Monday between 0 and 1 o'clock 23 things happened. Now I add a new parameter, so that the data looks somehow like that: Hour Day Freq Freq2 1 0 Mo23874 2 1 Mo20 476 3 2 Mo14201 4 3 Mo27 912 5 4 Mo26 172 Now I'd like to have a plot for every weekday containing the two frequencies as a line during the hours. Is this possible with two y-axes? Thanks for your help, Antje -Ursprüngliche Nachricht- Von: Deepayan Sarkar [mailto:[EMAIL PROTECTED] Gesendet: Montag, 9. Januar 2006 18:08 An: Antje Schüle Cc: r-help@stat.math.ethz.ch Betreff: Re: two y-axis in xy-plot On 1/9/06, Antje Schüle <[EMAIL PROTECTED]> wrote: > Hi there, > > > > I am wondering if it is possible to do an xyplot with two y-axes. I'd like > to print two parameters in a time series but they both have different > scales. > > > > Which parameter in xyplot can I add to achieve this result? The answer depends on the details of what you are doing, so please provide us with a reproducible example. Deepayan __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] label of second y-axis in xyplot (lattice)
Dear group,
First I provide you with an example, I found in the newsgroup. Then I'd like to
explain my problem to you by means of the output.
enviro <-
data.frame(Year = rep(2001:2002, each = 365),
Day = rep(1:365, 2),
Precip = pmax(0, rnorm(365 * 2)),
Temp = 2 + 0.2 * rnorm(365 * 2))
xyplot(Precip + Temp ~ Day | Year, data=enviro,
layout = c(1, 2),
panel = panel.superpose.2,
type = c('h', 'l'))
Now my question.
How can I achieve different labels for two y-axes? (Here this is not the case,
but the example should just visualize my question.)
So here in this case I'd like to have two labels. On the "normal" y-side
(axis2) the label = "Precip", on the other side (axis4) the label "Temp".
Thanks for your help.
Antje
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[R] R-help: conversion of long decimal numbers into hexadecimal
Hi there, could somebody help me to convert a decimal number into a hexadecimal number? I know that there is the function "sprintf", but the numbers I want to convert consist of 20 or more numbers. "Spintf" is not able to convert these big numbers. Thanks for any help. Antje [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] R-help: conversion of long decimal numbers into hexadecimal numbers
Hi there, could somebody help me to convert a decimal number into a hexadecimal number? I know that there is the function "sprintf", but the numbers I want to convert consist of 20 or more numbers. "Spintf" is not able to convert these big numbers. Thanks for any help. Antje Döring [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Comparing rows of matrices with different dimensions
Hi there, I have a question, which I thought is very easy to solve, but somehow I can't find a solution. Probably someone could help me quickly? Here it is: I have two matrices: a [,1] [,2] [,3] [1,]149 [2,]26 10 [3,]36 11 [4,]48 12 b [,1] [,2] [1,]14 [2,]25 [3,]36 Now I want to find out which rows of b can also be found in a (without its last column). So the solution must be something like either "TRUE FALSE TRUE" or the rows where their is a match (rows 1 and 3) Till now I have tried things like b %in% a[,1:2] or so but that doesn't work because I want to compare the WHOLE row of b with the whole row of a without column 3. Thank you very much for any help. Regards, Antje [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] problem with "parse"
Hi there again, I have a problem with the "parse"-command. First of all, I show you in a simplified way, what I am trying to do and what "R" answers: > test [1] "u.g$par1, u.g$par2" > mode(test) [1] "character" > ausdruck <- parse(text = test) Error in parse(file, n, text, prompt) : syntax error in "u.g$par1," That is what I did and I can't find the mistake. I just want to have "test" without quotes (to do eval(ausdruck) later) but somehow it doesn't work. Is there anything I have overlooked? Can't I put special characters like "$" or "," into this test-character? Thanks a lot for your help. Best, Antje [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
