[R] ERROR need finite 'ylim' values
David Winsemius
dwinsemius at comcast.net
Sun Jun 13 18:24:04 CEST 2010
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.
--
David.
--
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