Re: [circos] Column color error in Tableviewer

[Martin Krzywinski]

The error you are seeing is due to a "," included in the remove_cell_rx parameter in etc/parse-table.conf.

I included this character to strip away thousands-separators, but dimly forgot that it also reformats the color R,G,B values. Remove it to leave

remove_cell_rx = "'

I've cleaned up the code and have the latest version of the tableviewer here

http://mkweb.bcgsc.ca/export/tableviewer.tgz

Let me know whether this solves your problem.

I'm a bit swamped right now to release release a new version of the tools package.

Thanks for reporting the broken links. They are now fixed.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

On Wed, Nov 28, 2012 at 5:03 AM, Marco Herreras <marco.h...@gmail.com> wrote:

Hi, Martin,

First of all, many thanks for sharing this awesome tool. I am trying to use Tableviewer hurriedly for a master thesis, but I am willing to spend time learning how to use Circos afterwards, as I think I will be using it often.

After a lot of pain I managed to install it on Ubuntu 10.04 netbook edition, with Perl 5.10 (giving up for now installing it on OS X), ie gddiag and the example worked fine.

My table has some 137 rows and columns, with the same labels on rows and columns, both colored identically, with 6 different colors appearing in the first row and in the first column.

I used the first 75x75 submatrix of my 137x137 table with the online Tableviewer version to test the results (segments starting at 3 PM, colored by both rows and colors, no parallel labels, hide all ticks, etc). Everything worked fine and the result is great, but I need all 137 entities and most especially, I want the ribbons to show simple bilateral relationship; I prefer them to touch the segments everywhere, which I think is not available on the online version.

The trouble is, with the same csv file I uploaded for the online version (but containing the remaining rows and columns after the 75th), I am getting the error:

"Column color must be in r,g,b format (e.g. 100,50,150). The value (255170121) does not match this format.". [(255,170,121) is the first rgb color]

My Circos installation is not perfect yet: make-table and its man page do nothing, yet they did generate a table the first time I tried (I suspect a missing module, or else a problem after I executed the "> samples/table-basic-unique.txt" option)... 

Still, when executing "cat samples/table-unique.txt | bin/parse-table | bin/make-conf -dir data/" after tweaking the make-conf.conf file, it appears to be running, but I get the column color error.

I will reinstall Circos and try to save the data in txt instead of csv , but I'm fearing it is something relating to the csv file, not the installation... Can you please help? I am attaching a tweaked file (without the real names of the segments only because this file and its tableviewer rendition  summarize a lot of research...)

Many thanks in advance.

PS I think there is a broken link:

http://circos.ca/documentation/tutorials/utilities/visualizing_tables/

and

http://circos.ca/tutorials/lessons/utilities/visualizing_tables/?Visualizing_Tabular_Data_II

appear to point to the same contents...

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[Marco Herreras]

Hi, Martin, thanks for the quick reply.

It worked!

I had some trouble though, even after reinstalling everything again:

I had to set the remove cell parameter to ="" instead of = "' ; this last gave an error.

I got a missing chromosome error. I could not figure why that precise label among my table headers yielded the error, and not other headers, nor could I figure how the labels ended in karyotype.txt (some missing, some reordered)... setting the chromosomes order by karyotype parameter in circos.conf to no apparently solved it..

Finally, I got a missing character label error that made me remove all accents in my table headers, solving it. I'm sorry I didn't record the exact debug wording of the errors.

At last I generated an image, and instantly spotted a huge conceptual error in my table, so thanks again.

So, everything is working, except I have no clue as to how to set the ribbons to touch both segment ends and not just the row or column one.

My table is symmetrical, rows are each identical to respective columns, and table cells reflect a simple (bilateral, symmetrical) relation, diagonal terms being null...

Can you please help?

 

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[Martin Krzywinski]

> I have no clue as to how to set the ribbons to touch both segment ends and not just the row or column one.

The position of the ends of links is specified in the circos.conf file in the tools/tableviewer/etc directory. Specifically, it's being set by 'radius' and the <rule> which differentially changes radius1 (radius of link start).

<link>

ribbon           = yes

flat             = yes

file             = data/cells.txt

bezier_radius    = 0.0r

radius           = 0.999r-30p

thickness        = 1

color            = grey

stroke_color     = dgrey

stroke_thickness = 1

<rules>

<rule>

condition  = 1

radius1    = 0.999r-20p

</rule>

</rules>

</link>

To make both ends touch the segment, set

radius = 0.999r

and remove the <rules> block, or define

use = no

in the <rule> block to turn the rule off.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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[Marco Herreras]

Sorry for the delay acknowledging your answer. Many thanks! it worked as a breeze!

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[topialla]

Dear all,

be aware, that unfortunately the "," still is in the table-examples! So make sure, that you remove it (and of course do not use csv but tab-separated).

Best, Tobias