Re: [R] error while plotting
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. A, 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 __ 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.
Re: [R] error while plotting
-Original Message- From: Uwe Ligges [mailto:lig...@statistik.tu-dortmund.de] Sent: Tuesday, September 29, 2009 4:52 AM To: Nair, Murlidharan T Cc: r-help@r-project.org Subject: Re: [R] error while plotting 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. A, 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 Certainly I can plot mult.comp, but I only want to plot the significant ones so I parse the csv file to pick those that don't intersect the 0 line. I have saved the objects too. But there should be a way to plot it from the data saved in the csv file. It should have everything. I used to be able to do it with code that is giving me error. Some updates were made to the methods in R I guess 'plot' and I cannot get it to work anymore. Thanks for taking time to respond. I really appreciate it. Cheers../Murli __ 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.
Re: [R] error while plotting
I am trying to plot the confidence limits form multiple comparison analysis. How do I need to construct the object to plot it now. Thanks ../Murli -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 __ 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.
Re: [R] error while plotting
Perhaps you explain us how you really generate the data that are results from the multcomp package. Then it would probbaly be clear how to proceed. Uwe Ligges Nair, Murlidharan T wrote: I am trying to plot the confidence limits form multiple comparison analysis. How do I need to construct the object to plot it now. Thanks ../Murli -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 __ 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-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] error while plotting
-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. Cheers../Murli __ 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.
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 __ 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.
