run hangs on "drawing highlights and ideograms"

[Vahid Azimi]

Hi Martin,

I am attempting to make a circos plot, but the program keeps hanging on "drawing highlights and ideograms". I've attached my conf file and input data file, and was hoping you would be able to take a look at them and point me in the right direction.

Thanks so much in advance,
Vahid

[Martin Krzywinski]

I see that you don't have chromosomes_unit defined.

This parameter is therefore set to 1. If you have any definitions that use this value (e.g. tick spacing), then if Circos doesn't catch the fact that it needs to draw possibly millions of ticks, it will appear to hang.

Put

chromosomes_unit = 1000000

and see what happens.

Or comment out the tick.conf include.

In the future, please attach all the conf files, since the error may be caused by files you're importing via <<include>>.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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[Vahid Azimi]

Adding the chromosomes_units parameter did the trick. Thanks!

On Wednesday, April 1, 2015 at 11:22:16 PM UTC-7, Martin wrote:

I see that you don't have chromosomes_unit defined.

This parameter is therefore set to 1. If you have any definitions that use this value (e.g. tick spacing), then if Circos doesn't catch the fact that it needs to draw possibly millions of ticks, it will appear to hang.

Put

chromosomes_unit = 1000000

and see what happens.

Or comment out the tick.conf include.

In the future, please attach all the conf files, since the error may be caused by files you're importing via <<include>>.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

On Wed, Apr 1, 2015 at 4:00 PM, Vahid Azimi <vahid.a...@gmail.com> wrote:

Hi Martin,

I am attempting to make a circos plot, but the program keeps hanging on "drawing highlights and ideograms". I've attached my conf file and input data file, and was hoping you would be able to take a look at them and point me in the right direction.

Thanks so much in advance,
Vahid

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[Vahid Azimi]

Hi Martin,

I had another question, and figured I would ask here instead of creating a new thread.

I am trying to make a set of rules that assigns gene names (column 4 in the attached file "TCGA-A1-A0SE-01.circos.txt") a certain color based on the type of mutation (missense, nonsense, frameshift, etc.). The kicker is that I am trying to avoid displaying the text that indicates the mutation type (missense, nonsense, frameshift) on the CircOS diagram. I have read the tutorials on text rules -- unfortunately, I haven't come across anything to solve this problem. Are there any work-arounds that you may know of?

Thanks again,
Vahid

On Thursday, April 2, 2015 at 12:22:16 AM UTC-6, Martin wrote:

I see that you don't have chromosomes_unit defined.

This parameter is therefore set to 1. If you have any definitions that use this value (e.g. tick spacing), then if Circos doesn't catch the fact that it needs to draw possibly millions of ticks, it will appear to hang.

Put

chromosomes_unit = 1000000

and see what happens.

Or comment out the tick.conf include.

In the future, please attach all the conf files, since the error may be caused by files you're importing via <<include>>.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

On Wed, Apr 1, 2015 at 4:00 PM, Vahid Azimi <vahid.a...@gmail.com> wrote:

Hi Martin,

I am attempting to make a circos plot, but the program keeps hanging on "drawing highlights and ideograms". I've attached my conf file and input data file, and was hoping you would be able to take a look at them and point me in the right direction.

Thanks so much in advance,
Vahid

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[Vahid Azimi]

Update on my previous question -- I appended my input txt file gene names with specific symbols (e.g. ".", ",", "^", etc.) depending on the type of mutation, and was hoping to use rules to color each gene depending on which symbol it is associated with. I used the Text-Bubble tracks tutorial as a template to write my rules. However, I am getting the following error:

*** CIRCOS ERROR ***

  There was a problem evaluating the string [var(value) =~ /'/] as code (error:
  syntax error at (eval 4607) line 1, near "'ARRDC4'' =~ /'"



Please excuse my ignorance of the Perl programming language. I have attached the main conf file, the rules file, as well as the txt file containing my sample data.

Thanks,
Vahid

[Martin Krzywinski]

You can attach any number of parameters and values to each data point

e.g.

hs10 10 20 genea type=deletion,id=123

Then use the values of these parametesr in rules

<rules>

<rule>

condition = var(type) eq "deletion"

color = red

</rule>

</rules>

This tutorials shows one way to do this

http://circos.ca/documentation/tutorials/recipes/data_id/

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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[Vahid Azimi]

Worked like a charm. Thank you!

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