Visualising insertion distributions with IGoR about igor

[qmarcou]

Hi Will,
Indeed your three questions can be answered by a single answer:

• The in g.marginals[0]["even_nickname"] is a vector or higher order array of probabilities. Additional dimensions will be present in case the realization of the considered event is conditionally dependent on other events. g.marginals[1]["even_nickname"] will give you the order of the dimensions.
• As for realizations themselves there are three different properties you are referring to, it will be easier to understand for the case of gene choice as for the peculiar choice of insertions the 3 can be redundant:
  • R.name : the realization name, e.g for gene choices the name of the gene
  • R.value : the actual value associated with the realization name, e.g for gene choice the actual gene sequence
  • R.index: the realization index on the marginal array. So if you want the probability of the realization R just access ```g.marginals[0]["even_nickname"][R.index]` (note this only works with the 1 dimensional example, otherwise you will have to specify indices for the others dimensions too)

These properties are the same than the ones described for the C++ interface: https://github.com/qmarcou/IGoR#inference-and-evaluation-output

The fact that for insertions the 3 properties are equal is true only if the model has been constructed in a special way defining a range of authorized number of insertions. Bottom line: stick with using R.index even for insertions

Hope this helps