visualization incomplete vis_spec #419
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@@ Coverage Diff @@
## develop #419 +/- ##
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+ Coverage 77.95% 78.05% +0.10%
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Files 22 22
Lines 2141 2183 +42
Branches 506 517 +11
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+ Hits 1669 1704 +35
- Misses 345 355 +10
+ Partials 127 124 -3
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doc/example/example_Fujita/visuSpecs/.~lock.Fujita_visuSpec_2.tsv#
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petab/visualize/helper_functions.py
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| # DATASET_ID in vis_spec.columns: | ||
| # vis_spec[LEGEND_ENTRY] = vis_spec[DATASET_ID] | ||
| # else: | ||
| # vis_spec[LEGEND_ENTRY] = 'condition' |
petab/visualize/helper_functions.py
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| vis_spec[X_LABEL] = 'time' | ||
| if X_SCALE not in vis_spec.columns: | ||
| vis_spec[X_SCALE] = LIN | ||
| # TODO: Y_VALUES column will already be there? |
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what do you mean by this?
if it is not there it will be created right here
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I meant that maybe the code was reorganized in such a way that Y_VALUES will always be in vis_spec when check_ex_visu_columns is called. But now i think, that lines 575, 576 are still needed for the case when DATASET_ID is in vis_spec file but not Y_VALUES.
| vis_spec = pd.DataFrame(columns_dict) | ||
| else: | ||
| # TODO: do validation | ||
| # so, plotid is definitely there |
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validation meaning something like PLOT_ID in vis_spec.columns?
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ah I see. you could link this issue in the comment
| else: | ||
| # PLOT_ID is there, but NOT DATASET_ID and not Y_VALUES, | ||
| # but potentially some settings. | ||
| # TODO: multiple plotids with diff settings |
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this does not work with multiple plotIDs right now?
If it does not raise warning. If it does remove comment
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vis_spec like this won't work right now
| plotId | xOffset | yScale |
|---|---|---|
| plot1 | 100 | log |
| plot2 | 50 | log |
| plot3 | 0 | lin |
I don't know if anyone would want to use such vis_spec. Potentially could be tried to plot everything with different settings.
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and documentation_data_format.md is has still the old mandatory columns |
| vis_spec = pd.read_csv(visualization_file, sep="\t", index_col=None) | ||
| except pd.errors.EmptyDataError: | ||
| vis_spec = pd.DataFrame() | ||
| return vis_spec |
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maybe include warning? Usually users probably do not intend to have empty visu files
Personally I would put todos in an issue and remove them from example but maybe that is just a matter of taste |
minor typos in example notebooks remove temporary notebook file group import of warnings in helper_functions.py (codacy)
…into pl_visualization
…into pl_visualization
Now visualization should work with
In addition to that, two visualization examples are added: about plotting without vis_spec and with vis spec (closes Add commented example for creation of visualization files #272)