Re: [circos] Start [0] must be smaller than end [-66] coordinate in karyotype file ?

[Martin Krzywinski]

There are two problems with in your input file.

First, the tableviewer works on integer data only. This is a limitation that I hope at some point to remove. You'll need to multiply your values by some constant, e.g. 1000.

You also have a "*" character in one of the row names. The parser barfs when it sees this. 

I've adjusted the table file - attached and included the image. The full data/conf archive for this is at

http://mkweb.bcgsc.ca/tableviewer/tmp/mlhimjq/circos-tableviewer-mlhimjq.tar.gz

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

On Thu, Nov 1, 2012 at 8:59 PM, Archie Zheng <rebel...@gmail.com> wrote:

Hello gentlepeople，

I have got an ERROR REPORT, but i don't know what's that means.

Pls help me!

AN ERROR HAS OCCURRED. NO IMAGE HAS BEEN CREATED.

Circos image output (/home/martink/www/htdocs/tableviewer/tmp/fykvsgf/results/circos-table-fykvsgf-large.png) could not be found.

Don't panic. Read the error reports below and the hint section that explains what might be going wrong.

ERROR REPORTS

If your data is incorrectly formatted, the table parser will generate errors.

TABLE PARSER ERRORS

CIRCOS ERRORS

If the parser generated errors, Circos will also complain about missing files.

debuggroup summary 0.14s welcome to circos v0.63 25 Jun 2012 

debuggroup summary 0.14s loading configuration from file /home/martink/www/htdocs/tableviewer/tmp/fykvsgf/etc/circos.conf 
debuggroup summary 0.14s found conf file /home/martink/www/htdocs/tableviewer/tmp/fykvsgf/etc/circos.conf 

debuggroup summary 0.45s debug will appear for these features: summary 
debuggroup summary 0.45s parsing karyotype and organizing ideograms 


*** CIRCOS ERROR *** 

Start [0] must be smaller than end [-66] coordinate in karyotype file. 


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: 

TABLE DATA USED FOR FIGURE

miRNA
Omega-3
Omega-6

Control
rno-miR-874
0.071

0.066
0.002
rno-miR-211

0.098
0.069
0.005
rno-miR-3577
0.049
0.330
0.007

rno-miR-2985
0.032
0.350
0.007
rno-miR-133a
0.022

0.193
0.007
rno-miR-344a-5p

0.213
1.243
0.007
rno-miR-702-3p
0.059
0.385
0.008

rno-miR-3593-3p
0.001
0.082
0.009
rno-miR-206
0.008

0.066
0.009
rno-miR-375

0.013
0.115
0.011
rno-miR-185*
0.426
1.058
0.012

DISPLAY OPTIONS

• Row/column segments in descending order.
• Row/column segments ordered alphabetically by label.
• Row ribbons placed first.
• Cells for which row and column name are the same are hidden.
• Cells with small values are attenuated.
• Segment color is interpolated by segment count.
• False-color scheme applied to cell ribbons.
• Cell values sampled every 2.5% percentiles for color.
• Q1 quartile ribbons have transparency 3.
• Q1 quartile ribbons have no stroke.
• Q2 quartile ribbons have transparency 2.
• Q3 quartile ribbons have transparency 1.
• Ribbon colour sorce is set to row.
• Ribbon transparency set to 1/5.
• Ribbon fade transparency set to 0/5.
• Larger ribbons on top.

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[Archie Zheng]

Thanks for your kindly help, Martin.

That's works!

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