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I have the following Circos diagram, which I rendered as an SVG file and then converted to PNG, for the purposes of illustration:

Circos diagram

The text labels that circle the outer rim are oriented correctly from 12 o'clock to 9 o'clock, oriented outwards, away from the grey arcs.

Between 9 and 12, the text labels are oriented inwards, overlapping the grey arc. This is not expected.

Here's a close-up, to clarify the issue:

enter image description here

If I output a PNG from Circos, instead of SVG, the labels are drawn correctly, but then I lose the ability to mark up the vector-formatted SVG figure in Adobe Illustrator or Inkscape. So I need the SVG output.

Here's a snippet of the circos.conf file relevant to the addition of the labels:

<image>
dir = /tmp
file = circos.png
png = yes
radius = 3000p
background = white
angle_offset = -176
</image>

...

<plots>
<plot>
type                           = text
color                          = black
file                           = factorList.txt
r0                             = 1r
r1                             = 1r+200p
label_size                     = 12p
label_font                     = condensedbold
padding                        = 0p
rpadding                       = 0p
label_snuggle                  = yes
max_snuggle_distance           = 1r
snuggle_sampling               = 2
snuggle_tolerance              = 0.25r
snuggle_link_overlap_test      = yes 
snuggle_link_overlap_tolerance = 2p
snuggle_refine                 = yes
</plot>
</plots>

I'm not sure what other options I can apply to try to resolve this. My question is: What should I try in this or another configuration file, which fixes the SVG output? Thanks for your advice.

Alex Reynolds
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    Give enough information so that one can reproduce the problem on one’s own system. Point to some input data and tell how you invoke the program on the command line. – daxim Dec 13 '11 at 14:49
  • Instead of 'fixing' circos to output SVG properly, is it an option to post-process the SVG to find and rotate the incorrectly-rotated items? – Phrogz Dec 13 '11 at 17:08
  • @daxim: Thanks for offering to help, but as there are a number of configuration and data files involved, this question is probably easier to answer by people who have some familiarity with Circos. – Alex Reynolds Dec 14 '11 at 00:20

1 Answers1

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Maybe you can try this option:

label_rotate = no

And I think the layout above caused by the snuggle option ,and also check your conf file and be sure all the "r0" and "r1" of plot(type=text) are bigger than 1r .

Here is the circos lessonss example

Gentle Y
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    The better way to solve it is joining the circos mail list groups.google.com/group/circos-data-visualization .There Martin and circos users will help you directly . – Gentle Y Mar 12 '12 at 06:47