[R] Plot error in package lme4
Hi, I am new to R and not fantastic at statistics so it may well be that I am doing something silly but I can't figure out what it is and hoping that somebody can help. I am running package lme4, and trying to get a Residuals vs. Fitted graph. When I try to plot, I receive an error. Error in as.double(y) : cannot coerce type 'S4' to vector of type 'double' Here is the code I am using library(lme4) m1-lmer(y~trt*time*loc_block*Season+(1|ID), data=d) plot(m1,add.smooth=F,which=1) Error in as.double(y) : cannot coerce type 'S4' to vector of type 'double' I searched the forums for some answers but haven't found anything useful. Any insight into what I am doing wrong and how to fix it. Sara [[alternative HTML version deleted]] __ R-help@r-project.org 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] Plot error in package lme4
Sara Krause skkrause at gmail.com writes: Hi, I am new to R and not fantastic at statistics so it may well be that I am doing something silly but I can't figure out what it is and hoping that somebody can help. I am running package lme4, and trying to get a Residuals vs. Fitted graph. When I try to plot, I receive an error. Error in as.double(y) : cannot coerce type 'S4' to vector of type 'double' Here is the code I am using library(lme4) m1-lmer(y~trt*time*loc_block*Season+(1|ID), data=d) plot(m1,add.smooth=F,which=1) Error in as.double(y) : cannot coerce type 'S4' to vector of type 'double' I searched the forums for some answers but haven't found anything useful. Any insight into what I am doing wrong and how to fix it. Sara The standard diagnostics which you have seen in 'lm' are not implemented for 'lme4'. You have to do it yourself, but it's not *too* hard: library(lme4) ## from ?lmer fm1 - lmer(Reaction ~ Days + (Days|Subject), sleepstudy) f - fitted(fm1) r - residuals(fm1) plot(f,r) sm - loess(r~f) v - seq(min(f),max(f),length=101) lines(v,predict(sm,data.frame(f=v)),col=2) Further questions about lme4 should probably go to the r-sig-mixed-models mailing list. __ R-help@r-project.org 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] Plot error bars on skyline plot
Hi, I have generated a skyline plot of a tree in newick format using ape. How can I plot the error bars for this graph? I only have the the tree data. un-8.1:0, 20.1:0):0, 6.1:3):123, (35.1:0, (22.1:0, (43.1:1, 29.1:0):0):0):4, 25.1:6):0, ((42.1:0, 21.1:0):3, (39.1:0, 2.1:0):3):1):8, (3.1:0, 7.1:0):8):48, (15.1:0, 14.1:0):0, 11.1:0):0, 37.1:0):0, ((16.1:1, 30.1:0):0, 13.1:0):1):58, ((31.1:1, 19.1:0):18, 28.1:33):22):14):75):39, ((26.1:6, 17.1:8):60, (((41.1:0, 1.1:3):0, (9.1:0, 27.1:0):1):2, (5.1:0, 10.1:0):3):1, (38.1:1, (4.1:1, (24.1:0, 18.1:0):2):0):0):16, 36.1:19):8, (32.1:0, 33.1:1):29):33, (40.1:18, ((23.1:0, 12.1:1):3, 34.1:2):16):42):1):82); t-read.tree(text=un) # following example from ape package cl1 - collapsed.intervals(ci,0) cl2 - collapsed.intervals(ci,0.0119) sk1 - skyline(cl1) # from collapsed intervals sk1 - skyline(ci) # from coalescent intervals sk1 - skyline(tree.hiv) # from tree sk2 - skyline(cl2) # from collapsed intervals sk2 - skyline(ci, 0.0119) # from coalescent intervals sk2 - skyline(tree, 0.0119) # from tree plot(sk1, show.years=TRUE, subst.rate=0.0023, present.year = 2011, col=c(grey(.8),1)) lines(sk2, show.years=TRUE, subst.rate=0.0023, present.year = 2011) legend(.15,500, c(classic, generalized), col=c(grey(.8),1),lty=1 Thanks! [[alternative HTML version deleted]] __ R-help@r-project.org 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] plot error bars on skyline plot
Hi, I have generated a skyline plot of a tree in newick format using ape. How can I plot the error bars for this graph? I only have the the tree data. un-8.1:0, 20.1:0):0, 6.1:3):123, (35.1:0, (22.1:0, (43.1:1, 29.1:0):0):0):4, 25.1:6):0, ((42.1:0, 21.1:0):3, (39.1:0, 2.1:0):3):1):8, (3.1:0, 7.1:0):8):48, (15.1:0, 14.1:0):0, 11.1:0):0, 37.1:0):0, ((16.1:1, 30.1:0):0, 13.1:0):1):58, ((31.1:1, 19.1:0):18, 28.1:33):22):14):75):39, ((26.1:6, 17.1:8):60, (((41.1:0, 1.1:3):0, (9.1:0, 27.1:0):1):2, (5.1:0, 10.1:0):3):1, (38.1:1, (4.1:1, (24.1:0, 18.1:0):2):0):0):16, 36.1:19):8, (32.1:0, 33.1:1):29):33, (40.1:18, ((23.1:0, 12.1:1):3, 34.1:2):16):42):1):82); t-read.tree(text=un) # following example from ape package cl1 - collapsed.intervals(ci,0) cl2 - collapsed.intervals(ci,0.0119) sk1 - skyline(cl1) # from collapsed intervals sk1 - skyline(ci) # from coalescent intervals sk1 - skyline(tree.hiv) # from tree sk2 - skyline(cl2) # from collapsed intervals sk2 - skyline(ci, 0.0119) # from coalescent intervals sk2 - skyline(tree, 0.0119) # from tree plot(sk1, show.years=TRUE, subst.rate=0.0023, present.year = 2011, col=c(grey(.8),1)) lines(sk2, show.years=TRUE, subst.rate=0.0023, present.year = 2011) legend(.15,500, c(classic, generalized), col=c(grey(.8),1),lty=1 Thanks! [[alternative HTML version deleted]] __ R-help@r-project.org 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] Plot error
Hi guys, I am a newbie to R, so apologies in advance. I created this simple table in excel, saved in tab delimited .txt: name value_1 value_2 1 bill 14 2 ben 2 2 3 jane 3 1 test -read.table(\path\to\file, sep=\t, header=TRUE) x -c(seq[value_1]) y -c(seq[value_2]) plot(x,y) and i get this error Error in xy.coords(x, y, xlabel, ylabel, log) : (list) object cannot be coerced to type 'double' What does this mean and how do i fix it? Thanks for the help, James __ R-help@r-project.org 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] Plot error
Hi James, On Sat, Jul 17, 2010 at 2:50 PM, James Platt james-pl...@hotmail.co.uk wrote: Hi guys, I am a newbie to R, so apologies in advance. I created this simple table in excel, saved in tab delimited .txt: name value_1 value_2 1 bill 1 4 2 ben 2 2 3 jane 3 1 test -read.table(\path\to\file, sep=\t, header=TRUE) x -c(seq[value_1]) y -c(seq[value_2]) You lost me here. What is seq[value_1] supposed to do? Please fix your example. plot(x,y) and i get this error Error in xy.coords(x, y, xlabel, ylabel, log) : (list) object cannot be coerced to type 'double' What does this mean and how do i fix it? Thanks for the help, James __ R-help@r-project.org 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. -- Ista Zahn Graduate student University of Rochester Department of Clinical and Social Psychology http://yourpsyche.org __ R-help@r-project.org 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] Plot error
Hi James, I believe the issue has to do with the values you assigned to 'x' and 'y'. You call the function c() on seq[value_1], but you assigned your data not to 'seq' but to 'test'. You need to use the variable name that you assigned your data to (as a side note seq() is a function, so you should probably avoid using that as name to store data anyways). Also you have data in a variable 'test' that has both rows and columns, so the preferred way to access it is variablename[rowname/number , columnname/number]. In your case that would be test[ , value_1]. I left the space before the comma blank to indicate include all rows. It does technically work in this case to simply write test[value_1] but this is prone to error in other situations. This is my best guess as to what you want to do: #Read in Data #(just to make sure were on the same page) test - structure(list(name = structure(c(2L, 1L, 3L), .Label = c(ben, bill, jane), class = factor), value_1 = 1:3, value_2 = c(4L, 2L, 1L)), .Names = c(name, value_1, value_2), class = data.frame, row.names = c(NA, -3L)) test # print so we can look at it #Assign columns to variables 'x' and 'y' x - test[ , value_1] y - test[ , value_2] #plot plot(x, y) #Or using data directly plot(test[ , value_1], test[ , value_2]) Cheers, Josh On Sat, Jul 17, 2010 at 7:50 AM, James Platt james-pl...@hotmail.co.uk wrote: Hi guys, I am a newbie to R, so apologies in advance. I created this simple table in excel, saved in tab delimited .txt: name value_1 value_2 1 bill 1 4 2 ben 2 2 3 jane 3 1 test -read.table(\path\to\file, sep=\t, header=TRUE) x -c(seq[value_1]) y -c(seq[value_2]) plot(x,y) and i get this error Error in xy.coords(x, y, xlabel, ylabel, log) : (list) object cannot be coerced to type 'double' What does this mean and how do i fix it? Thanks for the help, James __ R-help@r-project.org 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. -- Joshua Wiley Ph.D. Student, Health Psychology University of California, Los Angeles http://www.joshuawiley.com/ __ R-help@r-project.org 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] Plot error
Hi both, Sorry my mistake I was trying to make a graph from another file I called seq, I decided to use test as an example, but mixed up the two. I have got this to work now thanks. after doing this: #Assign columns to variables 'x' and 'y' x - test[ , value_1] y - test[ , value_2] #plot plot(x, y) cheers, James On 17 Jul 2010, at 16:07, Joshua Wiley wrote: Hi James, I believe the issue has to do with the values you assigned to 'x' and 'y'. You call the function c() on seq[value_1], but you assigned your data not to 'seq' but to 'test'. You need to use the variable name that you assigned your data to (as a side note seq() is a function, so you should probably avoid using that as name to store data anyways). Also you have data in a variable 'test' that has both rows and columns, so the preferred way to access it is variablename[rowname/number , columnname/number]. In your case that would be test[ , value_1]. I left the space before the comma blank to indicate include all rows. It does technically work in this case to simply write test[value_1] but this is prone to error in other situations. This is my best guess as to what you want to do: #Read in Data #(just to make sure were on the same page) test - structure(list(name = structure(c(2L, 1L, 3L), .Label = c(ben, bill, jane), class = factor), value_1 = 1:3, value_2 = c(4L, 2L, 1L)), .Names = c(name, value_1, value_2), class = data.frame, row.names = c(NA, -3L)) test # print so we can look at it #Assign columns to variables 'x' and 'y' x - test[ , value_1] y - test[ , value_2] #plot plot(x, y) #Or using data directly plot(test[ , value_1], test[ , value_2]) Cheers, Josh On Sat, Jul 17, 2010 at 7:50 AM, James Platt james-pl...@hotmail.co.uk wrote: Hi guys, I am a newbie to R, so apologies in advance. I created this simple table in excel, saved in tab delimited .txt: name value_1 value_2 1 bill 14 2 ben 2 2 3 jane 3 1 test -read.table(\path\to\file, sep=\t, header=TRUE) x -c(seq[value_1]) y -c(seq[value_2]) plot(x,y) and i get this error Error in xy.coords(x, y, xlabel, ylabel, log) : (list) object cannot be coerced to type 'double' What does this mean and how do i fix it? Thanks for the help, James __ R-help@r-project.org 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. -- Joshua Wiley Ph.D. Student, Health Psychology University of California, Los Angeles http://www.joshuawiley.com/ __ R-help@r-project.org 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] Plot error
The other question I have: Is there any way to link the data point on the graph to the name of a row i.e in my table: name value_1 value_2 bill 14 ben 2 2 jane 3 1 I click on the data point at 2,2 and it would read out ben thanks again. James On 17 Jul 2010, at 16:43, James Platt wrote: Hi both, Sorry my mistake I was trying to make a graph from another file I called seq, I decided to use test as an example, but mixed up the two. I have got this to work now thanks. after doing this: #Assign columns to variables 'x' and 'y' x - test[ , value_1] y - test[ , value_2] #plot plot(x, y) cheers, James On 17 Jul 2010, at 16:07, Joshua Wiley wrote: Hi James, I believe the issue has to do with the values you assigned to 'x' and 'y'. You call the function c() on seq[value_1], but you assigned your data not to 'seq' but to 'test'. You need to use the variable name that you assigned your data to (as a side note seq() is a function, so you should probably avoid using that as name to store data anyways). Also you have data in a variable 'test' that has both rows and columns, so the preferred way to access it is variablename[rowname/number , columnname/number]. In your case that would be test[ , value_1]. I left the space before the comma blank to indicate include all rows. It does technically work in this case to simply write test[value_1] but this is prone to error in other situations. This is my best guess as to what you want to do: #Read in Data #(just to make sure were on the same page) test - structure(list(name = structure(c(2L, 1L, 3L), .Label = c(ben, bill, jane), class = factor), value_1 = 1:3, value_2 = c(4L, 2L, 1L)), .Names = c(name, value_1, value_2), class = data.frame, row.names = c(NA, -3L)) test # print so we can look at it #Assign columns to variables 'x' and 'y' x - test[ , value_1] y - test[ , value_2] #plot plot(x, y) #Or using data directly plot(test[ , value_1], test[ , value_2]) Cheers, Josh On Sat, Jul 17, 2010 at 7:50 AM, James Platt james-pl...@hotmail.co.uk wrote: Hi guys, I am a newbie to R, so apologies in advance. I created this simple table in excel, saved in tab delimited .txt: name value_1 value_2 1 bill 14 2 ben 2 2 3 jane 3 1 test -read.table(\path\to\file, sep=\t, header=TRUE) x -c(seq[value_1]) y -c(seq[value_2]) plot(x,y) and i get this error Error in xy.coords(x, y, xlabel, ylabel, log) : (list) object cannot be coerced to type 'double' What does this mean and how do i fix it? Thanks for the help, James __ R-help@r-project.org 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. -- Joshua Wiley Ph.D. Student, Health Psychology University of California, Los Angeles http://www.joshuawiley.com/ __ R-help@r-project.org 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. [[alternative HTML version deleted]] __ R-help@r-project.org 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] plot error
Hello All: I am having the following error message when I increase the resolution (res=30 to res=350) of my graph: Error in plot.xy(xy, type, ...) : ignoring SIGPIPE signal Calls: plot - plot.default - plot.xy Execution halted Here is the code: ofn - MAY11.png bitmap(ofn, type = png256, width = 21, height = 30, pointsize = 30, bg = white,res=350) If I change res=350 to res=30, everything is fine. par(cex.main=1.2,cex.lab=1.8,cex.axis=1.4) Does anybody have any comment please? Many thanks, Mohsen [[alternative HTML version deleted]] __ R-help@r-project.org 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] plot error
On 13.05.2010 16:49, Mohsen Jafarikia wrote: Hello All: I am having the following error message when I increase the resolution (res=30 to res=350) of my graph: Error in plot.xy(xy, type, ...) : ignoring SIGPIPE signal Calls: plot - plot.default - plot.xy Execution halted Here is the code: ofn- MAY11.png bitmap(ofn, type = png256, width = 21, height = 30, pointsize = 30, bg = white,res=350) If I change res=350 to res=30, everything is fine. par(cex.main=1.2,cex.lab=1.8,cex.axis=1.4) Does anybody have any comment please? Does not happen for me. This may be a ghostscript issue rather than an R issue, though. Hard to say since we do not know: your R version, OS, ghostscript version etc. Uwe Ligges Many thanks, Mohsen [[alternative HTML version deleted]] __ R-help@r-project.org 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@r-project.org 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] plot error
Hello All:
I am having the following error message when I increase the resolution
(res=30 to res=350) of my graph:
Error in plot.xy(xy, type, ...) : ignoring SIGPIPE signal
Calls: plot - plot.default - plot.xy
Execution halted
Here is the code:
ofn - MAY11.png
bitmap(ofn, type = png256, width = 21, height = 30, pointsize = 30, bg =
white,res=350) If I change res=350 to res=30, everything is
fine.
par(cex.main=1.2,cex.lab=1.8,cex.axis=1.4)
par(mfrow = c(6,3))
for(C in 1:18)
{
.
Does anybody have any comment please?
Many thanks,
Mohsen
[[alternative HTML version deleted]]
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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.
Re: [R] plot error -- figure margins too large
Ping-Hsun Hsieh wrote:
Hi,
I am trying to plot my dataset, consisting of one column with numeric values
and one column with group IDs.
The set is similar to the following df.
df - NULL
for ( i in 1:20)
{
tmp1 - runif(1000,0,5)
tmp2 - cbind(tmp1,i)
df - rbind(df,tmp2)
}
Now I would like to plot the numeric column, stratified by the group IDs, in a
single figure.
First, I partitioned the frame into a 1x20 array. Then I plot the numeric
values of each group in a sub-plot.
Note that only should the left most y-axis be shown, and the x-axis is only the
group numbers.
Also the margin between two sub-frame should be fairly small so it looks like
only one figure, rather than 20 figures.
The following codes were used to achieve my goal, but I got an error saying
figure margins too large.
cols - sample(rainbow(20))
par(mfrow=c(1,20))
for ( i in 1:20)
{
tmp - subset(df, df[,2]==i)
if(i!=1)
{
plot(df[,1],axes=F,col=cols[i],frame.plot=F,xlab=NA,pch=19,ylim=c(0,5))
mtext(i, line=1,side=1)
}
else{
plot(df[,1],axes=F,col=cols[i],frame.plot=F,xlab=NA,pch=19,ylim=c(0,5))
axis(2,at=0:5)
mtext(i, line=1,side=1)
}
}
I also tried to set the margins by modifying the _par_ command:
par(mfrow=c(1,20),mar=(4,2,4,0.05))
Still, received the same error.
The error depens on the space of your device. If your device is larger,
it might work. For a smaller device I'd try
df - matrix(c(runif(2,0,5), rep(1:20, each=1000)), ncol=2)
cols - sample(rainbow(20))
par(mfrow=c(1,20), oma=c(5,5,4,1), mar=rep(0, 4))
# nor margins (mar) for a single figure, but outer margins (oma)
for ( i in 1:20)
{
tmp - subset(df, df[,2]==i)
if(i!=1)
{
plot(df[,1],axes=F,col=cols[i],frame.plot=F,xlab=NA,pch=19,ylim=c(0,5),
ylab=)
mtext(i, line=1,side=1)
}
else{
plot(df[,1],axes=F,col=cols[i],frame.plot=F,xlab=NA,pch=19,ylim=c(0,5))
axis(2,at=0:5)
mtext(i, line=1,side=1)
}
}
or even better go with lattice that does the job for you.
The other experiment:
While I was using the following codes, it almost showed what I would like, but
the figure ended with only the last sub-plot. The only difference between the
two is I was attempting to add a main-label in the figure.
To add a main label, use the code above and add:
title(Multiple figures in a plot, outer=TRUE)
Uwe Ligges
cols - sample(rainbow(20))
par(mfrow=c(1,20),mar=c(4,0.05,3,0.05))
plot.new()
mtext(Multiple figures in a plot,line=1,at=13)
for ( i in 1:20)
{
tmp - subset(df, df[,2]==i)
if(i!=1)
{
plot(df[,1],axes=F,col=cols[i],frame.plot=F,xlab=NA,pch=19,ylim=c(0,5))
mtext(i, line=1,side=1)
}
else{
plot(df[,1],axes=F,col=cols[i],frame.plot=F,xlab=NA,pch=19,mar=c(4,4,3,0.05),ylim=c(0,5))
axis(2,at=0:5)
mtext(i, line=1,side=1)
}
}
Any suggestions and advices are welcome.
Thanks,
Mike
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__
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Re: [R] plot error -- figure margins too large
Thanks, Uwe.
You code does what I would like to have!
Best,
Mike
-Original Message-
From: Uwe Ligges [mailto:lig...@statistik.tu-dortmund.de]
Sent: Tuesday, September 29, 2009 1:36 AM
To: Ping-Hsun Hsieh
Cc: r-help@r-project.org
Subject: Re: [R] plot error -- figure margins too large
Ping-Hsun Hsieh wrote:
Hi,
I am trying to plot my dataset, consisting of one column with numeric values
and one column with group IDs.
The set is similar to the following df.
df - NULL
for ( i in 1:20)
{
tmp1 - runif(1000,0,5)
tmp2 - cbind(tmp1,i)
df - rbind(df,tmp2)
}
Now I would like to plot the numeric column, stratified by the group IDs, in
a single figure.
First, I partitioned the frame into a 1x20 array. Then I plot the numeric
values of each group in a sub-plot.
Note that only should the left most y-axis be shown, and the x-axis is only
the group numbers.
Also the margin between two sub-frame should be fairly small so it looks like
only one figure, rather than 20 figures.
The following codes were used to achieve my goal, but I got an error saying
figure margins too large.
cols - sample(rainbow(20))
par(mfrow=c(1,20))
for ( i in 1:20)
{
tmp - subset(df, df[,2]==i)
if(i!=1)
{
plot(df[,1],axes=F,col=cols[i],frame.plot=F,xlab=NA,pch=19,ylim=c(0,5))
mtext(i, line=1,side=1)
}
else{
plot(df[,1],axes=F,col=cols[i],frame.plot=F,xlab=NA,pch=19,ylim=c(0,5))
axis(2,at=0:5)
mtext(i, line=1,side=1)
}
}
I also tried to set the margins by modifying the _par_ command:
par(mfrow=c(1,20),mar=(4,2,4,0.05))
Still, received the same error.
The error depens on the space of your device. If your device is larger,
it might work. For a smaller device I'd try
df - matrix(c(runif(2,0,5), rep(1:20, each=1000)), ncol=2)
cols - sample(rainbow(20))
par(mfrow=c(1,20), oma=c(5,5,4,1), mar=rep(0, 4))
# nor margins (mar) for a single figure, but outer margins (oma)
for ( i in 1:20)
{
tmp - subset(df, df[,2]==i)
if(i!=1)
{
plot(df[,1],axes=F,col=cols[i],frame.plot=F,xlab=NA,pch=19,ylim=c(0,5),
ylab=)
mtext(i, line=1,side=1)
}
else{
plot(df[,1],axes=F,col=cols[i],frame.plot=F,xlab=NA,pch=19,ylim=c(0,5))
axis(2,at=0:5)
mtext(i, line=1,side=1)
}
}
or even better go with lattice that does the job for you.
The other experiment:
While I was using the following codes, it almost showed what I would like,
but the figure ended with only the last sub-plot. The only difference between
the two is I was attempting to add a main-label in the figure.
To add a main label, use the code above and add:
title(Multiple figures in a plot, outer=TRUE)
Uwe Ligges
cols - sample(rainbow(20))
par(mfrow=c(1,20),mar=c(4,0.05,3,0.05))
plot.new()
mtext(Multiple figures in a plot,line=1,at=13)
for ( i in 1:20)
{
tmp - subset(df, df[,2]==i)
if(i!=1)
{
plot(df[,1],axes=F,col=cols[i],frame.plot=F,xlab=NA,pch=19,ylim=c(0,5))
mtext(i, line=1,side=1)
}
else{
plot(df[,1],axes=F,col=cols[i],frame.plot=F,xlab=NA,pch=19,mar=c(4,4,3,0.05),ylim=c(0,5))
axis(2,at=0:5)
mtext(i, line=1,side=1)
}
}
Any suggestions and advices are welcome.
Thanks,
Mike
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[R] plot error -- figure margins too large
Hi,
I am trying to plot my dataset, consisting of one column with numeric values
and one column with group IDs.
The set is similar to the following df.
df - NULL
for ( i in 1:20)
{
tmp1 - runif(1000,0,5)
tmp2 - cbind(tmp1,i)
df - rbind(df,tmp2)
}
Now I would like to plot the numeric column, stratified by the group IDs, in a
single figure.
First, I partitioned the frame into a 1x20 array. Then I plot the numeric
values of each group in a sub-plot.
Note that only should the left most y-axis be shown, and the x-axis is only the
group numbers.
Also the margin between two sub-frame should be fairly small so it looks like
only one figure, rather than 20 figures.
The following codes were used to achieve my goal, but I got an error saying
figure margins too large.
cols - sample(rainbow(20))
par(mfrow=c(1,20))
for ( i in 1:20)
{
tmp - subset(df, df[,2]==i)
if(i!=1)
{
plot(df[,1],axes=F,col=cols[i],frame.plot=F,xlab=NA,pch=19,ylim=c(0,5))
mtext(i, line=1,side=1)
}
else{
plot(df[,1],axes=F,col=cols[i],frame.plot=F,xlab=NA,pch=19,ylim=c(0,5))
axis(2,at=0:5)
mtext(i, line=1,side=1)
}
}
I also tried to set the margins by modifying the _par_ command:
par(mfrow=c(1,20),mar=(4,2,4,0.05))
Still, received the same error.
The other experiment:
While I was using the following codes, it almost showed what I would like, but
the figure ended with only the last sub-plot. The only difference between the
two is I was attempting to add a main-label in the figure.
cols - sample(rainbow(20))
par(mfrow=c(1,20),mar=c(4,0.05,3,0.05))
plot.new()
mtext(Multiple figures in a plot,line=1,at=13)
for ( i in 1:20)
{
tmp - subset(df, df[,2]==i)
if(i!=1)
{
plot(df[,1],axes=F,col=cols[i],frame.plot=F,xlab=NA,pch=19,ylim=c(0,5))
mtext(i, line=1,side=1)
}
else{
plot(df[,1],axes=F,col=cols[i],frame.plot=F,xlab=NA,pch=19,mar=c(4,4,3,0.05),ylim=c(0,5))
axis(2,at=0:5)
mtext(i, line=1,side=1)
}
}
Any suggestions and advices are welcome.
Thanks,
Mike
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Re: [R] Plot error
Hi
r-help-boun...@r-project.org napsal dne 28.05.2009 16:21:01:
I want to plot data such that the 3 time points(a,b,c) lie on the
X-axis
and
the values of these times points are on Y-axis for n samples
(e.g.100).
So, I have an object x, dim 100 4, it is a dataframe (when checked the
class)
x =
name a b c
10.11 1.11 0.86
2 . . .
3 . . .
.
.
.
100
so when i say:
plot(1:3, x[,2:4], type=l) - I get the error below
Error in xy.coords(x, y, xlabel, ylabel, log) :
(list) object cannot be coerced to type 'double'
However if I do:
plot(1:3, x[1,2:4], type=l) -- It works for the 1st row, and
each
individual row BUT NOT ALL ROWS
Please could someone explain what is happening here?
I wonder if I need to use 'lines' for the remaining, BUT I have
another
dataset y with same dimensions as x, which I want to plot on the same
graph/plot to see the difference between x and y.
Your data looks like this:
x - data.frame(name=sample(letters, 10), a=runif(10), b=rnorm(10),
c=rlnorm(10))
The problem is that the subset x[,2:4] is also a data frame, not a
matrix.
class(x[,2:4]) #[1] data.frame
The simplest thing is probably to use lines, as you say.
row - seq_len(nrow(x))
xx - x[,2:4]
plot(row, xx$a, ylim=range(xx), type=l)
lines(row, xx$b, col=blue)
lines(row, xx$c, col=green)
Maybe also matplot is worth try
matplot(1:3,t(x[,2:4]))
regards
Petr
Regards,
Richie.
Mathematical Sciences Unit
HSL
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[R] Plot error
Hello, I am an R amateur. I want to plot data such that the 3 time points(a,b,c) lie on the X-axis and the values of these times points are on Y-axis for n samples (e.g.100). So, I have an object x, dim 100 4, it is a dataframe (when checked the class) x = name a b c 10.11 1.11 0.86 2 . . . 3 . . . . . . 100 so when i say: plot(1:3, x[,2:4], type=l) - I get the error below Error in xy.coords(x, y, xlabel, ylabel, log) : (list) object cannot be coerced to type 'double' However if I do: plot(1:3, x[1,2:4], type=l) -- It works for the 1st row, and each individual row BUT NOT ALL ROWS Please could someone explain what is happening here? I wonder if I need to use 'lines' for the remaining, BUT I have another dataset y with same dimensions as x, which I want to plot on the same graph/plot to see the difference between x and y. Thanks, NS -- View this message in context: http://www.nabble.com/Plot-error-tp23761408p23761408.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org 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] Plot error
I want to plot data such that the 3 time points(a,b,c) lie on the X-axis
and
the values of these times points are on Y-axis for n samples (e.g.100).
So, I have an object x, dim 100 4, it is a dataframe (when checked the
class)
x =
name a b c
10.11 1.11 0.86
2 . . .
3 . . .
.
.
.
100
so when i say:
plot(1:3, x[,2:4], type=l) - I get the error below
Error in xy.coords(x, y, xlabel, ylabel, log) :
(list) object cannot be coerced to type 'double'
However if I do:
plot(1:3, x[1,2:4], type=l) -- It works for the 1st row, and
each
individual row BUT NOT ALL ROWS
Please could someone explain what is happening here?
I wonder if I need to use 'lines' for the remaining, BUT I have another
dataset y with same dimensions as x, which I want to plot on the same
graph/plot to see the difference between x and y.
Your data looks like this:
x - data.frame(name=sample(letters, 10), a=runif(10), b=rnorm(10),
c=rlnorm(10))
The problem is that the subset x[,2:4] is also a data frame, not a matrix.
class(x[,2:4]) #[1] data.frame
The simplest thing is probably to use lines, as you say.
row - seq_len(nrow(x))
xx - x[,2:4]
plot(row, xx$a, ylim=range(xx), type=l)
lines(row, xx$b, col=blue)
lines(row, xx$c, col=green)
Regards,
Richie.
Mathematical Sciences Unit
HSL
ATTENTION:
This message contains privileged and confidential inform...{{dropped:20}}
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and provide commented, minimal, self-contained, reproducible code.
[R] plot error
HI there, why these lines of code are correct plot(count~spray, data = InsectSprays) plot(InsectSprays$count) but this return an error: plot(count, data = InsectSprays); data method is not implemented in plot?! Thanx, Gianandrea -- View this message in context: http://www.nabble.com/plot-error-tp19624873p19624873.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plot error
2008/9/23 glaporta [EMAIL PROTECTED]: HI there, why these lines of code are correct plot(count~spray, data = InsectSprays) plot(InsectSprays$count) but this return an error: plot(count, data = InsectSprays); data method is not implemented in plot?! The 'plot' function, like many functions in R, does different things depending on what its first parameter is... For plot(count~spray, data=InsectSprays) the first parameter is a formula, so what is really called is 'plot.formula'. This gets the names from the formula (count~spray) finds them in the 'data' parameter and does a plot. For plot(InsectSprays$count) you've taken the 'count' vector out of the data frame, so the ordinary plot function is called. If you do plot(count, data=InsectSprays), then 'count' here is just a bare word, so R looks up 'count' as an object, but doesn't find it (as long as there's no 'count' object in your workspace). You can do plot(~count, data=InsectSprays), but you get a slightly different plot than plot(count$InsectSprays). Compare and contrast the following: is=data.frame(count=runif(10),spray=runif(10)) plot(count,data=is) Error in plot(count, data = is) : object count not found plot(~count,data=is) plot(count~1,data=is) plot(is$count) Barry __ R-help@r-project.org 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] Plot error
Hi all, I'm trying to plot an svm model and I'm the following error: plot(model, data= dados[,-1], formula=formula(dados[,2]~dados[,3]),svSymbol = 1, dataSymbol = 2, symbolPalette = rainbow(4),color.palette = terrain.colors) Error in terms.default(x) : no terms component Anyone knows how to solve this??? Best regards, Pedro Marques __ R-help@r-project.org 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] Plot error
I'm trying to plot an svm model and I'm the following error:
plot(model, data= dados[,-1], formula=formula(dados[,2]~dados[,
3]),svSymbol = 1, dataSymbol = 2, symbolPalette = rainbow(4),color.
palette = terrain.colors)
Error in terms.default(x) : no terms component
Anyone knows how to solve this???
Asking the same question over and over again doesn't make it easier for us
to help you. Also, it is good form to point out which package you are
using (I presume this is svm in package e1071).
Please can you provide a reproducible example? (We don't have access to
the dados data.)
In the meantime, try typing traceback() after you get the error to see
where the problem is. Or, even better, install the debug package and step
through your code using mtrace.
Regards,
Richie.
Mathematical Sciences Unit
HSL
ATTENTION:
This message contains privileged and confidential inform...{{dropped:20}}
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