Unable to export publication quality graphics

[Liesa]

Hi all,

I am a new user of Cytoscape and am having trouble exporting
publication quality images. I found a thread "Saving high resolution
networks" started by Satish on May 4, and have tried the various
suggestions offered, but still cannot get a satisfactory image.
Specifically:

Exporting as a PDF doesn't offer me any choice of resolution, and
produces a poor quality image with illegible text.

Printing to a PDF produces the same result.

Exporting as SVG produces a file that I cannot open (have tried
repeatedly - error message says the file may be corrupt).

Exporting as EPS produces a file that opens in PDF format and the
image looks good - however, I can't do anything with it except open it
as a PDF. I tried opening the file in Powerpoint, where I am
assembling all my figures, and I get a placeholder rather than an
image (says the image will print to a postscript printer - mine
evidently doesn't qualify as only the placeholder prints). After
allowing the file to open as a PDF, I tried re-saving it as several
other image types (e.g. TIFF, PNG) and then opening them in
Powerpoint, but the resolution is lost by doing that. I also tried re-
saving the opened image as a PDF, then reopening in Adobe reader
(where it still looked good), using the snapshot tool to copy the
image, then pasting into Powerpoint, but once more, the resolution was
lost. I was able to open the file using Photoshop, but apparently the
image size was too big at 300 dpi and the clipboard export failed.

I tried exporting as a jpeg using advice given by Vijay in the
original thread. Increasing the zoom during the saving process did
indeed increase the resolution, but regardless of what the zoom is,
the image comes out with a black background instead of a white one.

Exporting as a PNG produces a file that I can't open (again, have
tried repeatedly- error message says the file may be corrupt).

Same for exporting as BMP.

I am using Cytoscape 2.6.3, which I assume to be an appropriate
version as I only downloaded it last week. I am also using a Mac (OS
10.4.11), if that makes any difference.

Can anyone help with this problem? Surely it's not meant to be this
hard.

Thanks,

Liesa

[Alexander Pico]

Hi Liesa,

It sounds like you've tried practically everything, but I'll describe how I
get high-res images into powerpoint and perhaps it will help.

1. Export > Network as Graphics
2. Select PDF and "Export text as font"
3. Open the PDF in Photoshop or Illustrator (300 pixels per inch works)
4. Save for web...
5. Select jpeg-high and make sure the image size is at least 1000 pixels in
the smallest dimension.
6. Drag and drop jpg into ppt.

I just did this now using 2.6.3. Attached are the pdf, jpg and ppt.
-Alex