Nair, Murlidharan T wrote:
-----Original Message-----
From: Uwe Ligges [mailto:lig...@statistik.tu-dortmund.de]
Sent: Sunday, September 27, 2009 1:17 PM
To: Nair, Murlidharan T
Cc: r-help@r-project.org
Subject: Re: [R] error while plotting
Nair, Murlidharan T wrote:
I am getting the following errors when I am trying to plot the data below. I
cannot figure out the error.
Error in plot.window(...) : need finite 'xlim' values
In addition: Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf
3: In min(x) : no non-missing arguments to min; returning Inf
4: In max(x) : no non-missing arguments to max; returning -Inf
#I am using the following code
#======================================================
library(multcomp)
sig.data<-structure(list(X = 1:10, Cell.lines = structure(c(2L, 5L, 8L,
9L, 3L, 6L, 10L, 1L, 4L, 7L), .Label = c("T(70%)a-N(0%)c", "T(70%)a-N(0%)f",
"T(70%)a-N(0%)i", "T(70%)c-N(0%)c", "T(70%)c-N(0%)f", "T(70%)c-N(0%)i",
"T(80%)a-N(0%)c", "T(80%)a-N(0%)f", "T(90%)-N(0%)f", "T(90%)-N(0%)i"
), class = "factor"), estimate = c(9859.74333, -5553.64802, 6227.17947,
8063.6472, 6548.86032, -8864.53103, 4752.7642, 9057.72021, -6355.67115,
5425.15635), lower = c(5560.57875, -9852.8126, 1928.01489, 3764.48262,
2249.69575, -13163.69561, 453.59962, 4758.55563, -10654.83573,
1125.99177), upper = c(14158.90791, -1254.48344, 10526.34405,
12362.81178, 10848.0249, -4565.36645, 9051.92877, 13356.88479,
-2056.50657, 9724.32092), p.val.raw = c(1.15e-08, 5.78e-05, 1.36e-05,
3.21e-07, 6.91e-06, 6.97e-08, 0.000331, 4.87e-08, 1.04e-05, 7.63e-05
), p.val.bon = c(2.66e-06, 0.0133, 0.00315, 7.41e-05, 0.0016,
1.61e-05, 0.0764, 1.13e-05, 0.0024, 0.0176), p.val.adj = c(2.65e-13,
0.000592, 2.82e-05, 9.72e-08, 6.56e-05, 8.76e-09, 0.0117, 6.22e-09,
6.44e-06, 0.000334)), .Names = c("X", "Cell.lines", "estimate",
"lower", "upper", "p.val.raw", "p.val.bon", "p.val.adj"), class = "data.frame", row.names = c("T(70%)a-N(0%)f",
"T(70%)c-N(0%)f", "T(80%)a-N(0%)f", "T(90%)-N(0%)f", "T(70%)a-N(0%)i",
"T(70%)c-N(0%)i", "T(90%)-N(0%)i", "T(70%)a-N(0%)c", "T(70%)c-N(0%)c",
"T(80%)a-N(0%)c"))
rownames(sig.data)<-sig.data[,2]
my.hmtest <- structure(list(
estimate = t(t(structure(sig.data[,"estimate"], .Names =
rownames(sig.data)))),
conf.int = sig.data[,4:5],
ctype = "ABCC4-2007"),
class = "hmtest")
par(mex=0.5) #This helps to accomodate the margins when text is getting cut off
plot(my.hmtest, cex.axis=0.7)
There is not method plot.hmtest defined anywhere. Hence plot.default is
used and that one does not know hoe to handle an object like the one you
just defined.
Uwe Ligges
Here is a little portion of the code that I used to generate the data.
amod<-aov(Expression~isoforms.name, data=z)
mult.comp<-glht(amod,linfct=mcp(isoforms.name="Tukey"))
conf.int<-confint(mult.comp,level=0.99)
p.value<-summary(mult.comp)$test$pvalues
out.data.mat<-data.frame(conf.int$confint[,1:3],p.value)
filename.csv<-paste(filename[i], "csv",sep=".")
filename.csv<-paste("csv",filename.csv,sep="/")
write.table(out.data.mat, file=filename.csv, sep=",", qmethod="double",
col.name=NA)
It is the csv file that I am trying to read and plot. Thanks for your help.
Ahhhh, again, the orgiginal code really helps to help:
A csv file does only contain the data values, all other structure of the
object is lost. You can either directly ask
plot(mult.comp)
after your second line, or in order to plot later on, use save() to save
the objects as an Rdata file and use load() to load it later on (e.g.
for plotting purposes.
Best,
Uwe Ligges
Cheers../Murli
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______________________________________________
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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.
