some text labels, not all, missing from drawing

[cb4circos]

Dear Martin,

I've looked at all such similar posts for a solution and none worked.  Pasted further below are my plot and ideogram sections...

Line #26 of the text input file is the first line of text input for which the corresponding label fails to appear in the drawing.  That line looks like this...

chrEBV_B_95_8_Raji_108401to171823_1to108400    30546    30929    Repeat_region

Yet the "-debug_group text" output shows nothing but normal processing for that text line input...

debuggroup text 6.81s label text 26 font default size 16 color black angle -35.525337120176 radius 1275 is_rotated 1 is_parallel 0 rotation 0
debuggroup text 6.81s labelpng text 26 x,y 3542 1765 angle,quadrant,offset -35.525337120176 0 0.337033997117647 textangle 35.525337120176 radius,offset 1275 0 w,h 23 15

As I type, I've just tried it with label_size = 8.  Thus, all labels finally show up (see attached), but I'd still prefer to use the original label_size =36.  Thus, I even tried a max_snuggle_distance  = 50r (the image took 455.35s to generate), but still no label stacking whatsoever.  Thus, I'm not sure which set of parameters to vary in order to attain label stacking.

Please advise.

Best,
CB

<plot>

type = text
file = <text input file name edited>
color = black

# on tick scale
r0 = 1r
r1 = 1r+200p

show_links     = yes
link_dims      = 2p,2p,150p,2p,2p
link_thickness = 2p
link_color     = red

padding        = 0p
rpadding       = 0p

label_size   = 36p
label_font   = condensed

label_snuggle         = yes
max_snuggle_distance  = 4r
snuggle_tolerance     = 0.25r
snuggle_sampling      = 2
snuggle_link_overlap_test = yes
snuggle_link_overlap_tolerance = 2p
snuggle_refine        = yes
</plot>

<ideogram>

<spacing>

default = 0u
break   = 0u

</spacing>

# thickness (px) of chromosome ideogram
thickness        = 20p
stroke_thickness = 2
# ideogram border color
stroke_color     = black
fill             = yes
# the default chromosome color is set here and any value
# defined in the karyotype file overrides it
fill_color       = black

# fractional radius position of chromosome ideogram within image
radius         = 0.50r
show_label     = no
label_font     = default
label_radius   = dims(ideogram,radius) + 0.05r
label_size     = 36
label_parallel = yes
label_case     = upper

# cytogenetic bands
band_stroke_thickness = 2

# show_bands determines whether the outline of cytogenetic bands
# will be seen
show_bands            = yes
# in order to fill the bands with the color defined in the karyotype
# file you must set fill_bands
fill_bands            = yes

</ideogram>

[Martin Krzywinski]

I've prepared an example that discusses this

http://mkweb.bcgsc.ca/export/text.snuggle.tgz

which works with the new v0.61 version. 

Previously, -debug_group textplace was intended to scan for text that was not being placed.

You can still use this, but I have also added overflow* parameters to force unplaced text to be drawn.

  overflow       = show

  overflow_font  = bold

  overflow_size  = 36

  overflow_color = red

Martin

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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[Martin Krzywinski]

This is due to a change in v0.61 in how axis parameters are defined.

Instead of axis* parameters, I now use <axes> blocks with one or more <axis> subblocks. This is more flexible and allows for greater variety in the image.

See this tutorial about it

http://mkweb.bcgsc.ca/dev/circos/documentation/tutorials/quick_guide/axes_and_backgrounds/

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

On Thu, Jun 14, 2012 at 2:23 PM, cb4circos <crlb...@gmail.com> wrote:

Martin,

Thanks for your response.  I can now see the overflow, but there's apparently a new problem in 0.61.  I had included 4 histogram plots included in the same drawing, and now unless I comment those histograms entirely :( I get the following error message:

  *** CIRCOS ERROR ***

  CONFIGURATION FILE ERROR

  Parameter [axis] of type [plot] is not supported.

  If you are having trouble debugging this error, use this tutorial to learn how
  to use the debugging facility

      http://www.circos.ca/tutorials/lessons/configuration/debugging

  If you're still stumped, get support in the Circos Google Group

      http://groups.google.com/group/circos-data-visualization

  Stack trace:

Please advise, thanks.

Best,
CB

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