[R] error while plotting

[Nair, Murlidharan T]

-----Original Message-----
From: Uwe Ligges [mailto:ligges at statistik.tu-dortmund.de] 
Sent: Sunday, September 27, 2009 1:17 PM
To: Nair, Murlidharan T
Cc: r-help at 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.

Cheers../Murli
 

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