Re: Trying to draw anything at all...

[Martin]

> but at this point it is irrationally annoying to me.

Circos was created for the bioinformatics community to visualize sequence annotations. This is why it has what may appear as idiosyncratic parameters, such as chromosomes and karyotypes. 

In hindsight, these weren't awesomely named.

> Eventually, I decide to just do everything like the tutorial, and realize I shouldn't have included the <ideogram> tags

Doesn't feel good creating something that has ruined someone's day. ;/

> Now I feel nihilistic,

Check the pdf/ directory in the distribution. You'll find a copy of Nietzsche's Ecce Homo. /jk

In an attempt to make the config very modular and introduce all sorts of whistling bells, I undercooked the error checking. 

If you're wondering how Circos will interpret your config, run it with -cdump flag. It will show you the full data structure (the color lists can be long, so you'll just have to mentally skip past those). You can also list a specific block or sub-block.

circos ... -cdump

circos ... -cdump ideogram

circos ... -cdump ideogram/spacing

On Monday, June 26, 2023 at 1:21:09 p.m. UTC-7 Lordoa wrote:

Hello,

For some lively context, a university research group hired me as their summertime trainee.
As the new official IT head™ in town, I have been given the duty of automating the drawing of circos plots.
For reference, nobody here has made it past installing perl.
Anyhow, I made a command line script to install everything, both strawberry perl and circos (and unzip them, can choose a local or global install).
Everything fine so far...

I start out my day, happy, thinking this will be a breeze. I end the day a broken man.

My initial config file starts bare-bones, and I begin my journey of error-driven-programming and fast googles and docs glancing.
Eventually it looks like this:
<image>
    <<include etc/image.conf>>
</image>
<<include etc/colors_fonts_patterns.conf>>
<<include etc/housekeeping.conf>>
<ideogram>
    <<include ideogram.conf>>
</ideogram>
karyotype = karyotype.txt

Modular™ is cool right?
Little did I know, little did I know...
For multiple hours, I then go mano a mano with this descriptive error message:
Use of uninitialized value $norm[0] in join or string at circos-0.69-9/bin/../lib/Circos/Unit.pm line 196, <F> line 4.
The 'from' parameter (undef) to Circos::Unit::unit_convert was an 'undef', which is not one of the allowed types: scalar...

Fun.
I start second guessing my data... Googling to no avail, consulting ChatGPT to no avail, even Bing. I even hop onto the .pm file and realize I don't know this programming language.
I then replace my data with the tutorial human chromosome data. Why is it hardcoded to be "chromosomes" anyway? Yes the docs specify that any data with co-ordinate positions is fine, but at this point it is irrationally annoying to me.
Eventually, I decide to just do everything like the tutorial, and realize I shouldn't have included the <ideogram> tags, or done the configuration directly in them.
Now I feel nihilistic, sitting as the last person in the office, everyone else having already left... writing this message...

Please save someone else from suffering the same fate (either error message, or documentation, I don't care...),
Cheers with water

[Lordoa]

Oh worry not, the message was intended to be humoristic. I'm glad that circos exists!