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rerender after moving to docs
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@bschilder
bschilder committed Apr 19, 2024
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2 changes: 1 addition & 1 deletion .gitignore
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/.quarto/
/agujournal2019.cls
/trackchanges.sty
/trackchanges.sty
2 changes: 1 addition & 1 deletion docs/index.html
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Expand Up @@ -1227,7 +1227,7 @@ <h3 class="anchored" data-anchor-id="supplementary-tables">Supplementary Tables<
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12 changes: 6 additions & 6 deletions docs/manuscript-preview.html
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Expand Up @@ -637,7 +637,7 @@ <h3 class="anchored" data-anchor-id="annotating-the-hpo-using-gpt-4">Annotating
<div id="fig-occurrence" class="quarto-figure quarto-figure-center quarto-float anchored">
<figure class="quarto-float quarto-float-fig figure">
<div aria-describedby="fig-occurrence-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca" class="">
<a href="manuscript_files/figure-html/fig-occurrence-1.png" class="lightbox" data-glightbox="description: .lightbox-desc-1" data-gallery="quarto-lightbox-gallery-1"><img src="manuscript_files/figure-html/fig-occurrence-1.png" class="img-fluid figure-img" width="768"></a>
<a href="manuscript_files/figure-html/fig-occurrence-1.png" class="lightbox" data-gallery="quarto-lightbox-gallery-1" data-glightbox="description: .lightbox-desc-1"><img src="manuscript_files/figure-html/fig-occurrence-1.png" class="img-fluid figure-img" width="768"></a>
</div>
<figcaption class="quarto-float-caption-bottom quarto-float-caption quarto-float-fig" id="fig-occurrence-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
Figure&nbsp;1: GPT-4 was able to annotate all human phenotypes based on whether they are always/often/rarely/never associated with different clinical characteristics. <strong>a</strong>, An example of the prompt input given to to GPT-4. The phenotypes listed in the second to last sentence (<em>italicised</em>) were changed to allow all HPO phenotypes to be annotated. <strong>b</strong>, Stacked bar plot showing the proportion of the occurrence of each clinical characteristic across all annotated HPO phenotypes. The terms shown on the x-axis are the clinical characteristics for which GPT-4 was asked to determine whether each phenotype caused them.
Expand Down Expand Up @@ -754,7 +754,7 @@ <h3 class="anchored" data-anchor-id="annotation-consistency-and-recall">Annotati
<div id="fig-checks" class="quarto-figure quarto-figure-center quarto-float anchored">
<figure class="quarto-float quarto-float-fig figure">
<div aria-describedby="fig-checks-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca" class="">
<a href="manuscript_files/figure-html/fig-checks-1.png" class="lightbox" data-glightbox="description: .lightbox-desc-2" data-gallery="quarto-lightbox-gallery-2"><img src="manuscript_files/figure-html/fig-checks-1.png" class="img-fluid figure-img" width="576"></a>
<a href="manuscript_files/figure-html/fig-checks-1.png" class="lightbox" data-gallery="quarto-lightbox-gallery-2" data-glightbox="description: .lightbox-desc-2"><img src="manuscript_files/figure-html/fig-checks-1.png" class="img-fluid figure-img" width="576"></a>
</div>
<figcaption class="quarto-float-caption-bottom quarto-float-caption quarto-float-fig" id="fig-checks-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
Figure&nbsp;2: GPT-4 annotations are consistent and accurate across annotations. <strong>a</strong>, Barplot showing the annotation consistency within phenotypes that were annotated more than once. In the lenient metric, annotations were collapsed into two groups (‘always’/‘often’ and ‘never’/‘rarely’). For a given clinical characteristic within a given phenotype, if an annotation was always within the same group it was considered consistent. In the stringent metric, all four annotation categories were considered to be different from one another. Thus, annotations were only defined as consistent if they were all identical. The blue dashed line indicates the probability of two annotations being consistent by chance in the lenient metric (~1/2). The gold dashed line is the probability of two annotations being consistent by chance in the stringent metric (~1/4). <strong>b</strong>, Bar plot of the true positive rate for each annotation. The labels above each bar indicate the number of phenotypes tested.
Expand Down Expand Up @@ -878,7 +878,7 @@ <h3 class="anchored" data-anchor-id="quantifying-phenotypic-severity">Quantifyin
<div id="fig-top-phenos" class="quarto-figure quarto-figure-center quarto-float anchored">
<figure class="quarto-float quarto-float-fig figure">
<div aria-describedby="fig-top-phenos-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca" class="">
<a href="manuscript_files/figure-html/fig-top-phenos-1.png" class="lightbox" data-glightbox="description: .lightbox-desc-3" data-gallery="quarto-lightbox-gallery-3"><img src="manuscript_files/figure-html/fig-top-phenos-1.png" class="img-fluid figure-img" width="768"></a>
<a href="manuscript_files/figure-html/fig-top-phenos-1.png" class="lightbox" data-gallery="quarto-lightbox-gallery-3" data-glightbox="description: .lightbox-desc-3"><img src="manuscript_files/figure-html/fig-top-phenos-1.png" class="img-fluid figure-img" width="768"></a>
</div>
<figcaption class="quarto-float-caption-bottom quarto-float-caption quarto-float-fig" id="fig-top-phenos-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
Figure&nbsp;3: Quantifying the severity of HPO phenotype annotations highlights the most impactful conditions. Heatmap of the top (n = 15), mid-range (n = 15), and bottom (n = 15) HPO phenotypes based on severity score. Severity scores were calculated by multiplying the numeric values assigned to each clinical characteristic according to <a href="#tbl-metric-weights" class="quarto-xref">Table&nbsp;2</a>. The average normalised score, representing overall phenotype severity on a 0-100 scale, was calculated by aggregating the multiplied values and normalising by the theoretical maximum severity score. The x-axis is scaled by the severity of the clinical characterisation.
Expand Down Expand Up @@ -1258,7 +1258,7 @@ <h3 class="anchored" data-anchor-id="supplementary-figures">Supplementary Figure
<div id="fig-severity-histo" class="quarto-figure quarto-figure-center quarto-float anchored">
<figure class="quarto-float quarto-float-fig figure">
<div aria-describedby="fig-severity-histo-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca" class="">
<a href="manuscript_files/figure-html/fig-severity-histo-1.png" class="lightbox" data-glightbox="description: .lightbox-desc-5" data-gallery="quarto-lightbox-gallery-5"><img src="manuscript_files/figure-html/fig-severity-histo-1.png" class="img-fluid figure-img" width="960"></a>
<a href="manuscript_files/figure-html/fig-severity-histo-1.png" class="lightbox" data-gallery="quarto-lightbox-gallery-5" data-glightbox="description: .lightbox-desc-5"><img src="manuscript_files/figure-html/fig-severity-histo-1.png" class="img-fluid figure-img" width="960"></a>
</div>
<figcaption class="quarto-float-caption-bottom quarto-float-caption quarto-float-fig" id="fig-severity-histo-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
Figure&nbsp;4: Distribution of the composite GPT-4 severity score of the severity scores for all HPO terms.
Expand All @@ -1279,7 +1279,7 @@ <h3 class="anchored" data-anchor-id="supplementary-figures">Supplementary Figure
<div id="fig-severity-boxplot" class="quarto-figure quarto-figure-center quarto-float anchored">
<figure class="quarto-float quarto-float-fig figure">
<div aria-describedby="fig-severity-boxplot-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca" class="">
<a href="manuscript_files/figure-html/fig-severity-boxplot-1.png" class="lightbox" data-glightbox="description: .lightbox-desc-6" data-gallery="quarto-lightbox-gallery-6"><img src="manuscript_files/figure-html/fig-severity-boxplot-1.png" class="img-fluid figure-img" width="768"></a>
<a href="manuscript_files/figure-html/fig-severity-boxplot-1.png" class="lightbox" data-gallery="quarto-lightbox-gallery-6" data-glightbox="description: .lightbox-desc-6"><img src="manuscript_files/figure-html/fig-severity-boxplot-1.png" class="img-fluid figure-img" width="768"></a>
</div>
<figcaption class="quarto-float-caption-bottom quarto-float-caption quarto-float-fig" id="fig-severity-boxplot-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
Figure&nbsp;5: Boxplot showing the relationship between composite severity score (y-axis) and the frequency response categories within each annotation type.
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window.onload = () => {
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