Revisions part 2 #4
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Replaces manually assigned clades with automated clade assignment based on mutations at sites previously associated with antigenic drift (Koel et al. 2013). This approach mimics how clades are assigned in practice, assigning new clade names when at least one epitope mutation occurs in a clade that has circulated at some minimum global frequency. Clade assignments almost always rely exclusively on genetic data, since the corresponding antigenic data require much more time to produce. This automated approach allows clades to be systematically reproduced and also tuned by adjusting the list of epitope sites and clade minimum frequency in the workflow configuration file.
We don't filter sequences by date, so remove the date filters from the configuration file.
Corrects the date fields for two early samples that were missing year information even though we know which years those samples were collected. Updates the data curation guide to reflect how to automate these corrections.
Append an incremental integer to recurrent clade names, so we can distinguish them in Auspice.
Adds logic to prevent tips of the tree from being assigned their own clade label.
Expands the x-axis label for the measurements panel to clarify that the values displayed in the panel are normalized distances from the reference strain rather than standard titer values.
Pushes the new tree with corrected rooting after fixing metadata for two samples. This tree and measurements panels also reflect new clade assignments where logic was refined to exclude tips in the tree from being considered their own clades.
Also, updates the x-axis labels for Fig 1C and D to more clearly describe the data being plotted.
Updates Fig 1C and D's vertical lines to match how Auspice renders these lines as solid for all thresholds.
Modifies the workflow to use the new `--threshold` interface in `augur measurements export` to add vertical lines at x=0 and x=2 in the measurements JSON.
Describes the specific effect of normalization in the methods. Also, removes a line about antigenic data in clade assignment that isn't relevant to the section.
2 tasks
Updates figures to reflect new clade assignments and new features of the measurements panel including the multiple vertical lines and the grouping of points by their coloring value.
Both vertical lines in panels C and D are solid lines now.
Adds a custom script and workflow rule that creates a measurements configuration JSON with predefined orderings for each grouping column such that grouping values are sorted by the clade of the reference strain in descending order of the earliest reference strain. This logic effectively orders reference strains (and all other grouping labels) by the order that clades appear in the tree such that the latest clades appear at the top of the measurements panel. Within each clade, grouping labels are ordered by the reference strain collection date in descending order so the latest references in the latest clade appear at the top.
Updates the text for case study 2 to reflect our new analysis with automated clade definitions and a focus on relatively newer data from clade 158N/189K. Although the details of alleles and measurements have changed for this case study, the original benefits of inspecting raw measurements and coloring by viral attributes like genotype remain.
This still wasn't as clear as it could have been, so these changes make the prior visualizations less ambiguous by specifying them.
Adds a description of how we order the grouping labels in the analysis for the paper with a configuration file and rewords the description of ordering in Results and Figure 2 caption to refer to the measurements export command's configuration file instead of the sidecar JSON output itself. This change minimizes the reference to "sidecar JSON" which is a bit of Nextstrain jargon.
Adds lines to Figure 4 between reference strains in the tree and the measurements panels on the right, to annotate the phylogenetic context of these strains. Updates the caption for Figure 4 to reflect the new clades and results represented in the figure.
Updates the results text for case study 1 and the corresponding caption in Figure 3 to reflect the new clades and measurements for those clades.
Updates Augur to reflect latest measurements functionality and removes a keyword argument to `read_node_data` that no longer exists.
Adds the version of Auspice that reflects all the features we mention in the paper.
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