Prepare proposal of plots and information to show (slide-based)

[priesgo]

Some ideas from our team meeting:

• [ ] Geographical distribution on a map. Challenge: both datasets are biased towards some few countries, we need to devise some normalisation to alleviate this issue. We can use plotly's ScatterGeo for this purpose (https://plotly.github.io/plotly.py-docs/generated/plotly.graph_objects.Scattergeo.html)
• [ ] Top recurrent mutations not in the lineage consensus. Implement a similar table to the top recurrent mutations table, but in this case showing only those mutations observed in a certain lineage that are not described as being part of the lineage. Rationale: these mutations may correspond to technical artifacts or show lineage evolution.
• [ ] Compare two lineages. Venn diagram between both mutations sets
• [ ] Consensus sequence across all samples belonging to the same lineage. We would need to recalculate the consensus every time a new sample is coming in. It would be useful to also compare it with the described consensus sequence. Any difference between both sequences may be due to technical artifacts or legitimate lineage evolution

[priesgo]

Results from discussion on 10.01.2023

Selection of alternative lineages

Two alternatives:

• Combo box with multiple selection and search
• Top 10 with check boxes

We need the annotations with readable lineage names

Geographical plot

Show pie plots over countries in a similar way to NextStrain. Size of circle is the prevalence of the lineage in a country When more lineages are selected the circle becomes a pie with different colors

Needleplot

Height will be the frequency X-axis genomic coordinates, full genome view Two colors for consensus and non-consensus mutations Threshold of frequency

Mirror option for second lineage

Heatmap comparison multiple lineages (to be named)

Threshold with minimum consensus in each lineage percentage)

We don't all genomic positions, but rather mutated positions Each row one lineage (>2) Color represents frequency or alternatively just a binary value yes/no (easier to interpret)

Sequence view

This is only useful for smaller regions (ie: domains or maybe genes) The size of each letter is the frequency