finding the plot limits generated by default

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

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_schwartz at 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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