Closed ArtPoon closed 3 months ago
Looks like the molecular clock model residuals are off as well.
Default display has been switched back to divergence by @GopiGugan
recoded.json
and lineage-specific Newick files from Paphlagon to my local machine for some testingmake_beadplots
function in batch_utils.py
badly needs some refactoring, will split it into multiple functions at least.new branch iss497
56a0786d30e18aeda59d2ba4ba1d6da16e89b0a6
I'll try to wrap up some of this refactoring and then I may need to hand this off to someone else
@GopiGugan can you please retrieve by_lineages
from the database and run it through the make_beadplots
function, and send me a CSV of the summary stats and predicted number of infections for each lineage?
Obtained CSV from @GopiGugan, will analyze
Summary stats seem reasonable:
Scatterplot of predicted number of infections (from HUNePi model) against sample size (number of sequences):
The issue seems to be that there is a small number of outlier lineages with very high predicted numbers of infections. For the diagnostic summary_stats.csv
data that @GopiGugan sent me, the maximum predicted number is about 4.4 million, but most of the predicted numbers fall within the range of 10 to 100,000. On a linear scale, this causes most lineages to be coloured purple/blue:
A log-transform on mapping predicted numbers of infections to the colour scale should resolve this on the front end
Ok this is fixed, tree colours look much better: