Custom chromosome number and size defined by users.

[MarilyneSummo]

Hi,

I am currently working on a form to generate custom visualizations with ideogram. Until now I was working on known species, but I would like to offer the possibility to users to choose the number of chromosomes to draw and their sizes.

I'm trying to change the value of the global variable chrBands to display custom chromosomes but if I understand correctly, ideogram still has to rely on an existing json file (by configuring dataDir or by retrieving the json from the internet) and so my chrBands variable is overwritten after my call to ideogram.

I would like to skip this step by having for example the possibility to define the value of chrBands in the config for unknown organisms.

Is it possible to add this option in the config? Or is there another way to fully customize the chromosomes without using a json file?

[eweitz]

Would it help if I extended the chromosomes API option to accept an array of objects, each including a name and length?

Also, out of curiosity, where are you using Ideogram?

[MarilyneSummo]

Yes it would be very useful. The format of chrBands seemed to me to be the most adapted to take into account the informations of centromeres (if available) and the particular cases like aneuploidy.

I work at CIRAD, in France, on the detection of genetic mosaicism in plants.

[mrouard]

Hello Eric,

This feature would be very useful as it may allow to skip a node.js server set up for ideogram. Is that correct?
Many thanks