54 smooth lineages plot #58
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Added a drop-down menu in lineages tab to select size of smoothing (default=14 days) Updated citation link in acknowledgement tab to point to published article
…informatics/covigator into 54-smooth_lineages_plot
Set default smoothing window to 14 days
| logger.debug("Getting data on samples by country...") | ||
| data = self.queries.get_accumulated_lineages_by_country( | ||
| data_source=data_source, countries=countries, lineages=lineages) | ||
| graph = dcc.Markdown("""**No data for the current selection**""") | ||
| if data is not None and data.shape[0] > 0: | ||
| logger.debug("Prepare plot on samples by lineage...") | ||
| lineages = list(data.sort_values("cumsum", ascending=False).lineage.unique()) | ||
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| data.set_index('date', drop=False) |
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I think this line is not doing anything, as set_index() does not affect the DataFrame on which it is called unless inplace=True is passed.
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Good hint. I thought I had already removed the line
| sma_df = sma_df.reset_index(level='lineage')[['ratio_per_date', 'cumsum', 'count']] | ||
| # Update columns with moving average over selected period | ||
| smooth_data.loc[:, 'ratio_per_date'] = sma_df['ratio_per_date'] | ||
| smooth_data.loc[:, 'cumsum'] = sma_df['cumsum'] |
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I was wondering if we want to do the rolling average also on cumsum and count considering that these values are only shown in the hover data, hence they do not affect the looks of the plot. What do you think? I don't have a strong preference here, just wondering.
| html.A("https://doi.org/10.1101/2021.02.04.429765", | ||
| href="https://doi.org/10.1101/2021.02.04.429765", target="_blank"), | ||
| html.A("https://doi.org/10.1371/journal.pone.0249254", | ||
| href="https://doi.org/10.1371/journal.pone.0249254", target="_blank"), |
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Nice one! :) thanks
covigator/dashboard/tabs/lineages.py
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| dcc.Markdown("""Select time period for smoothing"""), | ||
| dcc.Dropdown( | ||
| id=ID_DROPDOWN_PERIOD, | ||
| options=[{'label': c, 'value': c} for c in range(1, 32)] + [{'label': 'Disable', 'value': False}], |
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I suggest you set the label to "{} days".format(c) so it is more explicit what the numbers correspond to.
Incorporation of the suggestions for improvement from @priesgo
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