circos course basic example : ideogram borders and ticks messed up

[v singh]

Hi All,

I downloaded the circos course : http://circos.ca/tutorials/course/

and was following the examples but have run into a problem. While trying the very basic ideogram example located in 

folder : circos-course-0.61/workstation/2/1

I get the .png figure with uneven ideogram border and missing ticks on last chromosome (please see attached figure), which is in very different from original figure included in the course. 

My Linux distro is -- Linux version 2.6.32-279.22.1.el6.x86_64 (gcc version 4.4.6 20120305 (Red Hat 4.4.6-4) (GCC) ) #1 SMP Wed Feb 6 03:10:46 UTC 2013

I have not changed anything in the configuration files. Can anyone give me an idea as to why this might be happening??

-------------------------------------------------------

circos.conf file

-------------------------------------------------------

karyotype = ../data/karyotype.5chr.txt

chromosomes_units           = 1000000

chromosomes_display_default = yes

<<include ideogram.conf>>

<<include ticks.conf>>

<<include ../../etc/image.conf>>

<<include etc/colors_fonts_patterns.conf>>

<<include etc/housekeeping.conf>>

----------------------------------------------------------------

 ideogram. conf file

----------------------------------------------------------------

<ideogram>

<spacing>

default = 2u

#default = 10u

#<pairwise chr1>

#spacing = 5u

#</pairwise>

#<pairwise chr1 chr2>

#spacing = 2u

#</pairwise>

#<pairwise chr1 chr5>

#spacing = 25u

#</pairwise>

</spacing>

<<include ../../etc/ideogram.conf>>

</ideogram>

-------------------------------------------------------

ticks.conf file

-------------------------------------------------------

show_ticks          = yes

show_tick_labels    = yes

<ticks>

label_font      = default

radius          = dims(ideogram,radius_outer)

label_offset    = 5p

label_size      = 8p

multiplier      = 1e-6

color           = black

thickness       = 1p

<tick>

spacing        = 1u

size           = 5p

show_label     = no

</tick>

<tick>

spacing        = 5u

size           = 8p

show_label     = no

grid_start     = 0.5r

grid_end       = 0.975r

grid_color     = black

grid_thickness = 2p

show_grid      = yes

</tick>

<tick>

spacing        = 10u

size           = 12p

show_label     = yes

label_size     = 16p

format         = %d

</tick>

</ticks>

[Martin Krzywinski]

You're doing nothing wrong. The problem is an anti-aliasing bug in libgd. I've seen it before. Lines with thickness=1 when drawn with anti-aliasing create rectangular artefacts in the image.

You can turn anti-aliasing off in Circos. How to do this is described in this tutorial

http://circos.ca/documentation/tutorials/configuration/png_output/

Or, you can get a different version of libgd for your system. Unfortunately, I don't have a sense which versions have this bug. 

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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[v singh]

Thanks a ton for your prompt response! It is working beautifully now. I am sorry for raising an already addressed issue, should have searched for errors/bugs specific to png images.

Best regards