Paul Johnson wrote:
For many plots in a sub directory "PlotFigures", I have 2 versions,
one in eps version and  one in pdf version.

With Lyx-1.5.3 on Fedora Linux 8, I'm using a koma-script book format.
 I've run up against this problem inserting graphics.  When I insert a
pdf figure, then in the DVI/postscript output, the output is not good
because there's a big blank area at the top of the figure.  In the pdf
output, the document is good (presumably because the figure was pdf,
the latex processor handles it well).  On the other hand, if I insert
the eps figure in Lyx, then the DVI/postscript output is good, but the
pdf output looks bad.

I think this is happening because there really is a big white area at
the top of the pdf files, and I will have to remedy that for future
figures.

But for working with the existing images, what is a good approach?
I've been reading lyx-user archives.

In some email messages from this list, I see users ask this question
and they are advised to omit the image type from the LyX insert.  LyX
will use eps for DVI output and pdf for pdf output.  I mean, if a
graphic is available as Plot-001.eps or Plot-001.pdf,   then one
should simply insert the figure name "Plot-001" and the LaTeX
processor will choose the correct format. However, when I try that in
LyX, I see "figure not found" on the screen.

What's up with that?

In retrospect, I see I need to do more work in the R script that
manufactures the images, because I think I can stop the pdf output
from including that giant white space at the top of the pdf.  But it
seems weird to have to do that in order to get an EPS output file.


Have you tried specifying a clipping region in LyX? Might be there's an issue with reading the bounding box info from the PDF (or EPS) (or both).

/Paul

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