Peter Ehlers wrote: > > Giuseppe, > > See comments below. > > On 2010-06-13 10:24, David Winsemius wrote: >> >> >> Giuseppe wrote: >>> >>> Hello: >>> I use R with MAC >>> I have a simple data table, numeric and text columns, named dt. The >>> table >>> is imported through read.csv from a csv file. Row numbers are >>> automatically assigned, header is set to TRUE. there are 599 rows and >>> several columns. >>> >>> I am trying to plot using the stripchart command: one numeric variable >>> (say dt$fnatg) vs a text column (say dt$pat). dt$pat contains one of 3 >>> values: "pos", "neg", "" >>> >>> So I issue the following command: >>> >>>> stripchart (dt$fnatg~dt$pat) >>> >>> and works well. it works well also with several options and nuances: >>> >>>> stripchart (dt$fnatg ~ dt$pat, method ="jitter", jitter = 0.3, vertical >> =TRUE,log="y", pch=1, ylab="Thyroglobulin (ng/mL)",xlab="Surgical >> Pathology") >>> >>> Now I want my graph to exclude values for which dt$pat == "" >>> >>> I tried: >>> >>>> stripchart (dt$fnatg ~ dt$pat, method ="jitter", subset (dt, >> dt$pat!=""),jitter = 0.3, vertical =TRUE,log="y", pch=1, >> ylab="Thyroglobulin >> (ng/mL)",xlab="Surgical Pathology") >>> >>> there is no effect: the plot contains the same values as before >>> >>> the I tried first subsetting the table: >>> >>>> patonly<-(dt, dt$pat!="") which works well in creating a new table >> excluding the unwanted rows. I have noticed that the new table keeps the >> same row numbers assigned in the previous table. So row numbers now go 1 >> to >> 599 but with some intervals (for example there is no row 475 etc.). >>> >>> then I use: >>> >>>> stripchart (patonly$fnatg ~ patonly$pat, method ="jitter", jitter = >>>> 0.3, >> vertical =TRUE,log="y", pch=1, ylab="Thyroglobulin >> (ng/mL)",xlab="Surgical >> Pathology") >>> >>> and I get the following error: >>> >>> Error in plot.window(...) : need finite 'ylim' 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 f I try the same command but I use another text variable (for example >>> patonly$gr) in the same table to split the plot, it now works: >>> >>>> stripchart (patonly$fnatg ~ patonly$gr, method ="jitter", jitter = 0.3, >> vertical =TRUE,log="y", pch=1, ylab="Thyroglobulin >> (ng/mL)",xlab="Surgical >> Pathology") >>> >>> >>> My question is two fold: >>> Why does not the subset command work within the stripchart command? >>> >>> Why the subsetted table cannot be used in the stripchart command, when >>> the >>> plotting variable is the same previously used in the subsetting process? >>> >>> >> >> You appear to have adopted a strategy of using positional matching. >> Naming >> your arguments will often result in more informative error messages. >> Looking at the help page for stripchart, it appears that there is no >> "subset" parameter to set in any of its methods and only the formula >> method >> has a data argument. It should work with: >> >> stripchart(formula1 , data=subset(dta, subset=criteria), ....<rest of >> arguments preferably named> ) >> >> Your other option might be to use the with() function: >> >> with( subset(patonly, pat!=""), stripchart(fnatg ~ gr, ...<named >> arguments>) ) >> >> >> HTH. and if it doesn't, then submit a reproducible data example to work >> with. > > Actually, Giuseppe appears to have stumbled upon a bug in the > stripchart() function. > > First, here's a fix: > After your command > > patonly<-(dt, dt$pat!="") > > which I assume is meant to be > > patonly <- subset(dt, dt$pat!="") > > and which can be written as > > patonly <- subset(dt, pat!="") > > you should issue this: > > patonly$pat <- factor(patonly$pat) > > which will remove the empty level; stripchart() should > work well after that (and do use the data= argument > rather than dt$...). > > Alternatively, you could change your "text" variables > (which I assume are factors) to character values (or > re-import your data with stringsAsFactors = FALSE). > > > Now for the bug in stripchart(): > If the *first* group of the grouping variable is > empty, then stripchart() has a problem determining > the range of data values (x-values for horizontal > charts, y-values otherwise). I can replicate your > problem withe OrchardSprays dataset: > > # this works: > stripchart(decrease ~ treatment, data = OrchardSprays, > subset = treatment != "B") > > # this doesn't > stripchart(decrease ~ treatment, data = OrchardSprays, > subset = treatment != "A") > > I'll be submitting a bug report (and I think the fix > is easy). > > -Peter Ehlers > > ______________________________________________ > 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. > > Thank you Peter, both your solutions worked for me. Why do you insist for using data = argument? Giuseppe Giuseppe -- View this message in context: http://r.789695.n4.nabble.com/ERROR-need-finite-ylim-values-tp2253388p2253767.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.
