Thank you for your reply, but I have additional questions. I agree that
getting the common ranges before plotting would be the best scenario, it is
just complicated by the fact that the first plot is generated with a
function where all the data is passed in and within the function the data is
subset and plotted so I don't have control over the parameters of the plot.
That is why I am trying to just make the second plot (the one I have
complete control over) match up. I tried the par("usr") but am having an
odd result. Below is from my R console.
> par(mfrow=c(2,1))
> drawGffPlots2(data1,data2,trackingDye=TRUE,slice="chr13",newDev=0)
NULL
> par("usr")[1]
[1] 14215173
>
plot(densities_subset$V4,densities_subset$V6,type="h",xlim=c(par("usr")[1],par("usr")[2]),xlab="Position",ylab="Gene
Density")
> par("usr")[1]
[1] 10062761
This creates two rows, runs the function which populates the first row, then
I check the parameter you suggested so that I may use it for the second
plot. I then pass it to plot(), but the axes still don't line up so I check
the same parameter after the second plot has been drawn and it is very
different. Should par("usr")[1] not be exactly the same the second time I
display it as I passed it as the minimum for the second plot? Any help
would be appreciated.
- Fincher
On Fri, May 14, 2010 at 11:45, Marc Schwartz <marc_schwa...@me.com> wrote:
> On May 14, 2010, at 9:59 AM, Justin Fincher wrote:
>
> > I have two datasets that I would like to plot in a single figure. The
> first
> > plot is generated by a function that then takes a subset of the data.
> (It
> > is biological data so it is usually by chromosome e.g.
> > function(data1,subset="chr8") ) Since not only are the chromosomes
> different
> > sizes, but across different datasets there may be different numbers of
> > points for a single chromosome, I do not know the coordinates on the
> x-axis
> > prior to running the function.
> >
> > I want the scale of the second plot to align to that of the first, but I
> > don't know how to find the default xlim for the graph generated by the
> > function. Is there any way to access this information so I can then pass
> it
> > to the plot() of the second plot? Thanks!
> >
> > - Fincher
>
>
> The result of par("usr") will give you the actual limits of the x and y
> axes (plot region) once the first graphic is drawn to the device. See ?par
> for more information. Note that by default, R will extend the data ranges by
> 4% (see 'xaxs' in ?par).
>
> However, you are better off getting the common ?range of the relevant
> values in both subsets of data before plotting and then explicitly set the
> same x and y axis ranges in each plot by using the 'xlim' and 'ylim'
> arguments to plot().
>
> HTH,
>
> Marc Schwartz
>
>
>
> --
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>
>
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