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update from upstream nextstrain/auspice (#8)
* make frequencies tend to 0 in absense of data * increase padding value for frequencies * lint appeasment * set frequencies explicity to 0 if total is too low * reduce frequency normalizaton threshold to single constant * remove unassigned variable * Allow continuous colorings to define anchor points The schema currently allows datasets to provide a scale for non- continuous scales where specific trait values are given colour hexes (missing values are given greys by auspice). Here we extend this to continuous scales by interpreting the same data structure as anchor points which we interpolate between using the same method as we currently use for generating default continuous color scales (d3's `interpolateRgb`) * Allow legend entries to be user-defined This allows continuous colour scales to define custom legend entries, via a `legend` key in the JSON. This allows control over the values in the scale which we use as legend elements, the displayed text, and the range of values which each entry covers. Bounds are enforced to be non-overlapping. If overlapping bounds are detected, we revert to Auspice dynamically generating these. (This is a requirement for future work which will map continuous tip values to a legend entry, which will allow pie-chart display using the legend swatches.) * Legend bound matching is (a, b] for continuous scales This restores the algorithm used to associate a hovered legend item to tips for continuous variables. Commit 0f37b1a (Mar 2018) incorrectly changed this to `tip \in [a, b]` rather than the intended (and documented) `tip \in (a, b]`. This takes on more importance given that the previous commit allows user-defined bounds. Note that the frequencies panel already used `(a, b]` matching, so now the legend matching mirrors this. * Extend user-provided legend info beyond continuous scales * Use filterOptions to modify search alg * GitHub Action to create nextstrain.org PR This action will run on each auspice PR and create a corresponding PR on nextstrain.org which includes a commit using the version of auspice from this (auspice) PR. This functionality is extremely useful for auspice development as it will allow us to use a Heroku review app to test auspice in the context of nextstrain.org There are a number of future improvements to implement: * New auspice releases (tagged commits on `release` branch) would ideally create a PR on nextstrain.org which could be merged to update the version of auspice there. * Other consumers of auspice (e.g. auspice.us) could be added to this GitHub Action. * Allow non-continuous scatterplot variables This implements a requested improvement to the original scatterplot implementation. The implementation hinges on two changes: (1) The collection of values for a given variable (e.g. x-var) need to be computed and passed to PhyloTree to act as the scale's domain. We reuse the colorScale machinery here, which could be optimised (see todo messages in code), but this has the advantage that the domain ordering matches the legend (unless user supplied). (2) PhyloTree needed to be modified to use non-linear scales, in this case `pointScale`. This commit should be fully functional, however there are some future improvements to be made: (i) Grid text is obscured and unreadable when there are many entries in the domain. (ii) Genotypes and Boolean scales are not yet available. (iii) Jitter should be added to nodes to avoid obfuscation. * Layout changes occur via redux thunk This commit is in preparation for allowing genotype to be a scatterplot variable. This will complicate the allowable scatterplot variables and force these to update upon colorBy changes. This is much cleaner if layout is changed in a thunk. * Allow genotype to be scatterplot variable Genotype is treated differently to other colorings in two important ways: (1) it can change value, for instance when changing the colorby to another genotype position and (2) it is stored in a different place to other colorings. These require scatterplot logic to be more complex as actions are no longer separate - we now require a NEW_COLOURS action to potentially update the layout which was formerly within the remit of the CHANGE_LAYOUT actions. This is achieved through a middleware layer. This implementation makes it clear that jitter and better domain spacing are crucial for scatterplots. * Improve padding for categorical scatterplot variables This prevents nodes falling on the axis itself or at the very end of the grid, which was especially noticeable for traits with small domains. * Add jitter to categorical scatterplots * Apply clipping to first column of legend We have had issues in the past with legend values from column 1 overflowing into column 2. For instance, issue nextstrain#899 was fixed by PR nextstrain#914 which implemented a maximum character limit for legend names. This solution can produce misleading views, such as those described in nextstrain#1306. This solution implements a clipping mask for column 1, avoiding the complication of limiting the string size. Column 2 already has similar behaviour because the SVG element of the legend itself performs the clipping. * changelog * version bump to 2.26.0 for release * Always show regression toggle for clock layout Fixes a bug where the ability to toggle regression lines was hidden for clock views. (The ability to hide this toggle is only intended for scatter layouts, where we should not expose the toggle unless both axes are showing continuous variables.) * Adjust grayscale color ramp The existing grayscale color ramp (used for values absent in an explicitly specified color scale) had values that were too dark and threw off the overall color balance. This commit narrows the grayscale color ramp to be more in line with pastel color ramp. * Inject a bit of color into the "grayscale" color ramp This adds a bit of blue into the grayscale color ramp. Still reads as mostly gray, but no colors seem to exist more in the same universe as canonical auspice color ramp. * changelog * version bump to 2.27.0 for release * Styling adjustments to footer text * Remove metadata download from GISAID datasets This commit uses dataProvenance in metadata to identify datasets using "GISAID" data. For these datasets, the full metadata download is swapped to an "acknowledgments" download that only includes the following fields: - strain - gisaid_epi_isl - genbank_accession - originating_lab - submitting_lab - author * Cleanup metadata headers This commit cleans up naming of metadata headers in downloaded metadata TSV. It does the following: 1. Keeps headers as input into "augur export" rather than renaming by title. Thus it has "originating_lab" rather than "Originating lab", "pango_lineage" rather than "PANGO lineage", etc... This should make it easier for people to process downloaded metadata from Auspice alongside metadata provisioned by Nextstrain (via GISAID or via S3). 2. Makes "date" the second column as this is often what's most important. I couldn't figure out a way to intelligently order remaining fields. My first thought was to use metadata.colorings, but this isn't sorted. 3. Fixes "accession". It had been exporting as "[object Object]". * Update changelog * version bump to 2.28.0 for release Co-authored-by: Richard Neher <richard.neher@unibas.ch> Co-authored-by: James Hadfield <hadfield.james@gmail.com> Co-authored-by: james hadfield <jameshadfield@users.noreply.github.com> Co-authored-by: Muhammad Aditya Hilmy <mhilmy@hey.com> Co-authored-by: Trevor Bedford <trevor@bedford.io>
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