tickmarks on the inside on y axis and on the outside on the x axis

Hi

 

I got both axis doing one or the other, but cannot make one do ticks on the
inside while the other does it on the outside.

Use axis to draw them separately.  For example,

plot(rnorm(10),rnorm(10), axes=FALSE)
axis(1)
axis(2, tcl=0.5)
box()

You may also want to use the mgp parameter to axis to place the labels 
somewhere else.

Duncan Murdoch