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zero fractional infectivity plateaus fit with fixtop will draw curves outside bounds #59

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ckikawa opened this issue Apr 10, 2024 · 0 comments · Fixed by #60
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@ckikawa
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ckikawa commented Apr 10, 2024

Curves fit with fixtop with neutralizing titers outside the bounds of the assay draw curves immediately before the first point (lower bound). This is potentially confusing, since it looks like neutralization is being extrapolated outside the range of dilutions tested in the assay. Curvefits like these are more of a visual issue, since these data and the inferred curves call NT50s as being on the upper or lower bounds, which is the correct quantitative behavior. Example below:
image

These curves were inferred with fixtop = [0.75,1] and fixslope = [0.8,10]. The bottoms of curves are default fixed to 0. Corresponding curvefits and the raw fractional infectivity values:
frac_infectivity.csv
curvefits.csv

@jbloom jbloom linked a pull request Apr 11, 2024 that will close this issue
jbloom added a commit that referenced this issue Apr 11, 2024
Added the ``draw_in_bounds`` option to the curve plotting so that curves never are plotted outside the data range. Addresses [this issue](#59).
jbloom added a commit to jbloomlab/seqneut-pipeline that referenced this issue Apr 11, 2024
Draw neutralization curves using `draw_in_bounds=True` with `neutcurve` to avoid lines extrapolating beyond data. Addresses [this issue](jbloomlab/neutcurve#59).
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