You have mixed your x with your y, try this:

 
map("worldHires","Antarctica",ylim=c(-90,-60),xlim=c(-180,180),col="gray90",fill=TRUE)

I tend not to use maps/mapdata if I can help it (there are problems as
you can see, though there is support for projections with mapproject,
see ?map), if you want to use an alternative try this.

library(maptools)
data(wrld_simpl)
## select out just the continent
antarctica <-  wrld_simpl[wrld_simpl$NAME == "Antarctica", ]
plot(antarctica)
degAxis(1)
degAxis(2)

For a better display of this part of the world

library(rgdal)
## define a sensible projection
pr <- "+proj=laea +lat_0=-90 +ellps=WGS84 +datum=WGS84 +no_defs +towgs84=0,0,0"
antarctica.laea <- spTransform(antarctica, CRS(pr))


plot(antarctica.laea)

Removing the dud coordinates at -90 is a bit more difficult, but can
be done (the first plot by map() has a similar problem).

There is a mailing list R-Sig-Geo which is more topical for questions
like this if you want to explore further.

Cheers, Mike.

On Wed, Jun 5, 2013 at 11:00 PM, ejb <ejb...@psu.edu> wrote:
> Hey, I'm new with R and I'm attempting to map and then plot points on a map
> of Antarctica with help from some code at the following link.  Link
> <http://www.molecularecologist.com/2012/09/making-maps-with-r/>
>
> After downloading the packages here is the code I used. I feel like the
> problem has to do with the coordinates since I get a very small image that
> appears to be only a small portion of the continent (I want the whole
> thing). Thanks in advance!
>
> library(maps)
> library(mapdata)
> map("worldHires","Antarctica",xlim=c(-90,-60),ylim=c(-180,180),col="gray90",fill=TRUE)
>
>
>
>
>
>
>
> --
> View this message in context: 
> http://r.789695.n4.nabble.com/Map-Antarctica-tp4668713.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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-- 
Michael Sumner
Hobart, Australia
e-mail: mdsum...@gmail.com

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