circos heatmap

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Xiaofei Wang

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Feb 13, 2017, 10:39:50 PM2/13/17
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Dear there,

I am using circos to generate heatmap. But I got something wield. Here is the screenshot for my figure. For the circled part, why they do not they look neat?

For the circle on chr1, why the beginning of the different tracks do not start from 0? For the circle on 5th chromosome, why there is something look like spikes and the tracks look like with outlier, and also there is the same thing on other chromosomes?
 

Also, I want to add centromere on my figure. Here is the code in the configure file and the format in my centromeres.txt file, but why the centromeres are not drawn in the figure?

<highlights>
    ideogram = yes
    <highlight>
        file       = ../data/centromeres.txt
        stroke_thickness = 1
        stroke_color = black
        fill_color = blue
        z = 10
    </highlight>
</highlights>

Chr.    Pos.1   Pos.2

1       23443076        23443987

2       32102317        32103319

......



Thank you so much!

Best,

Xiaofei

Xiaofei Wang

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Feb 14, 2017, 3:30:18 PM2/14/17
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> Also, I want to add centromere on my figure. Here is the code in the configure file and the format in my centromeres.txt file, but why the centromeres are not drawn in the figure?

I figured it out. I gave wrong chromosomes name for centromeres.txt file.

X

Xiaofei Wang

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Feb 28, 2017, 3:08:18 PM2/28/17
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Dear Martin,

I still did not figure it out for the spikes that are in my heat map. Is it a bug or the problem with my coding? I have checked my code again and did not find something wrong. Could you let me know?

Also, I may check with old version of circos.

Thanks a lot!

Best,

Xiaofei

On Monday, February 13, 2017 at 5:39:50 PM UTC-5, Xiaofei Wang wrote:

Xiaofei Wang

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Mar 7, 2017, 5:26:41 PM3/7/17
to Circos
I just tried with different versions of circos, but still get the same problem. What is the possible reason in my case? It looks like outliers, but I did not find any abnormal thing in my data file, e.g., it is just the positions (or regions) for chromosomes.

Could you shed some light?

Thank you so much!

Best,

X

Martin Krzywinski

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Mar 7, 2017, 11:52:42 PM3/7/17
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Please post your data and conf files.



Martin Krzywinski
science + art


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Xiaofei Wang

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Mar 9, 2017, 9:36:34 PM3/9/17
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I attached my configure file and some of my data, if it is not enough, please let me. Thank you so much! Best, X

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circos.conf
centromeres.txt
karyotype.txt
gene.wiggle
genef.wiggle
karyotype.txt

Xiaofei Wang

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Mar 20, 2017, 2:45:03 PM3/20/17
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Dear MartinAny ideas why does this happen? Thanks a lot! 

On Tuesday, March 7, 2017 at 6:52:42 PM UTC-5, Martin wrote:
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Martin Krzywinski

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May 2, 2017, 11:11:17 PM5/2/17
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I'm not seeing this effect when I run your example.

You didn't include all your data/conf files. So I had to reconstruct some of your configuration. 

I've attached a working example.

m


Martin Krzywinski
science + art


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xia.tgz
circos.png

Xiaofei Wang

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May 3, 2017, 2:27:14 AM5/3/17
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It is wield. Which version did you use?

Thanks!

Xiaofei


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Martin Krzywinski

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May 4, 2017, 8:50:52 PM5/4/17
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Martin Krzywinski
science + art


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Xiaofei Wang

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May 15, 2017, 2:46:54 PM5/15/17
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It is so wired. I used the exactly same thing that you attached here. But, here is I got, still the same problem. I am thinking if it is the problem with the versions of dependencies.





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Xiaofei Wang

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May 15, 2017, 3:43:00 PM5/15/17
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which version did you use for Perl?


On Thursday, May 4, 2017 at 4:50:52 PM UTC-4, Martin wrote:
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Martin Krzywinski

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May 19, 2017, 8:49:14 PM5/19/17
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I've seen a similar kind of thing before long time ago with some versions of libgd. Strange artefacts appeared in the image due to an anti-aliasing but in the library.

To check whether this is the case, turn anti-aliasing off.

Do this either in 

etc/housekeeping.conf

via the anti_aliasing parameter, which is by default set to "yes", or in your circos.conf, like this

anti_aliasing* = no

with the "*" in the name telling Circos to override the value of the parameter included from housekeeping.conf.

m




Martin Krzywinski
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