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This is a page containing some information about the project. | ||
# tfpbrowser | ||
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## About | ||
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The Transmission Fitness Polymorphism Browser (tfpbrowser) is a visualisation tool for output from | ||
the Transmission Fitness Polymorphism Scanner (tfpscanner)[1-3]. Information on the visualisation | ||
options can be found below, while details regarding installation of the tfpbrowser package and the | ||
source code can be found at | ||
[https://github.com/mrc-ide/tfpbrowser](https://github.com/mrc-ide/tfpbrowser). | ||
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Six different visualisations can be accessed by selecting from the ‘View’ dropdown menu on the | ||
left-hand side. If the ‘View’ option is not visible, then the left-hand side menu may need to be | ||
expanded by clicking on the double arrow button. | ||
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### Tree Visualisations | ||
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There are four different tree visualisation options. These are described below, but a number of | ||
characteristics are common to each tree visualisation: | ||
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- The size of the circles (for internal nodes) and triangles (tips) indicates the size of the | ||
cluster that they represent. | ||
- The colour indicates a particular characteristic of the cluster. | ||
- On the right-hand side of each tree visualisation, the colouring of the bars indicates whether a | ||
genotype (for which a key mutation is labelled) is present (true) or absent (false) in the clusters | ||
at the same vertical level. | ||
- Further information on each cluster can be viewed by hovering over it with the mouse cursor. | ||
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The four tree visualisation options in the ‘View’ menu are: | ||
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#### Tree Clock Outlier | ||
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Displays a phylogenetic tree with clusters colour coded (key at the top) according to the value of | ||
the molecular clock outlier (MCO) statistic. This is computed by the tfpscanner as a measure of the | ||
degree to which evolutionary rates differed in the lineage leading to a phylogenetic cluster. | ||
Root-to-tip regression is used to predict the divergence of tips in a cluster and contrasts this | ||
with divergence within an ancestral clade including the given cluster. This predicted divergence is | ||
then compared to the true divergence of the cluster. | ||
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#### Tree Logistic Growth Rate | ||
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Displays a phylogenetic tree with clusters colour coded (key at the top) according to the value of | ||
the logistic growth rate. This is computed in the tfpscanner using one of two different methods | ||
depending on the level of model support calculated using the Akaike Information Criterion (AIC) and | ||
‘relative likelihood’. The first method uses a generalised linear model (GLM) to calculate the log | ||
odds of a sample being from a cluster of interest compared to a geographically and temporally | ||
matched sample weighted by prevalence, and multiplied by the estimated mean generation time to | ||
calculate the relative LGR per generation for each cluster of interest. The second method uses a | ||
generalised additive model (GAM) combined with a Gaussian process model to identify changes in | ||
growth rates over time. | ||
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#### Tree Mutations | ||
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This visualisation has a ‘Mutation’ menu from which to select a particular mutation to be | ||
highlighted in the phylogenetic tree. Clusters containing the mutation selected will be coloured red | ||
in the phylogenetic tree while clusters not containing this mutation will be grey. | ||
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#### Tree Sequences | ||
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This visualisation has a ‘Sequence’ menu from which to select a particular sequence ID. Clusters | ||
containing this sequence will be coloured red in the phylogenetic tree while those not containing it | ||
will be grey. | ||
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### Scatter plots | ||
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The molecular clock outlier and logistic growth rate statistics can also be viewed in scatter plots: | ||
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#### Sina Clock Outlier | ||
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Displays a scatter plot of the molecular clock outlier statistic value for each phylogenetic cluster | ||
on the y-axis and the lineage and/or mutation is stratified along the x-axis. The plot marker | ||
colours indicate the lineage and/or mutation and the size indicates the cluster size, both as per | ||
the legend on the right-hand side of the plot. _See ‘Tree Clock Outlier’ above for details of the | ||
molecular clock outlier statistic_. | ||
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#### Sina Logistic Growth Rate | ||
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Displays a scatter plot of the logistic growth rate value for each phylogenetic cluster on the | ||
y-axis and the lineage and/or mutation is stratified along the x-axis. The circle colours indicate | ||
the lineage and/or mutation and the size indicates the cluster size, both as per the legend on the | ||
right-hand side of the plot. _See ‘Tree Logistic Growth Rate’ above for details of this statistic_. | ||
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### Downloads | ||
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Tables, plots and .rds files can also be downloaded by clicking on the ‘Cluster statistics’ tab and | ||
selecting the relevant option. | ||
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### References | ||
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[1] Volz EM, Boyd O. Transmission Fitness Polymorphism Scanner. Available from: | ||
https://github.com/mrc-ide/tfpscanner | ||
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[2] Volz EM. Fitness, growth and transmissibility of SARS-CoV-2 genetic variants. Nat Rev Genet | ||
2023. https://doi.org/10.1038/s41576-023-00610-z | ||
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[3] Drake KO, Boyd O, Franceschi VB, Colquhoun RM, Ellaby NAF, Volz EM. Phylogenomic early warning | ||
signals for SARS-CoV-2 epidemic waves. eBioMedicine 2024: 100. | ||
https://doi.org/10.1016/j.ebiom.2023.104939 |