tiny-plot: inclusive/exclusive filters for classes in DGE scatter plots#264
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taimontgomery merged 14 commits intomasterfrom Dec 18, 2022
Merged
tiny-plot: inclusive/exclusive filters for classes in DGE scatter plots#264taimontgomery merged 14 commits intomasterfrom
taimontgomery merged 14 commits intomasterfrom
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… class filtering. These are mutually exclusive arguments. Class filters are applied before subsetting points by P value. scatter_by_dge and scatter_by_dge_class are now separate functions
…t users can change filters between resume runs
…r comment cleanup
…n is now listed before the control
…s in scatter_dge_class plots now that the counts index includes the classifier. I had kept this in earlier changes for the sake of allowing the interface to be changed. After some thought I think the net benefit of doing so isn't worth it
…ull handling case for scatter_by_dge to handle the edge case of a single None list element. Honestly, the later is fairly unlikely. The former is very likely with the new class filtering option
…dge_class can handle empty dataframe inputs for counts and dge values. Really this is only a concern with scatter_by_dge_class due to the new filters, but thought it was wise to include similar checks for scatter_by_dge
…t to be consistent with other filters in the project (e.g. GFF source and type filters)
…s and filters are case-insensitive in the project, so this makes sense for consistency and user-friendliness
…2.1 Run Configs (eek). Also added a fix (which I could have sworn I included earlier) that ensures the class list doesn't turn into a YAML anchor in the processed run config. Otherwise, it would still work for editing between replots but might be confusing to the user. This is an exciting feature though and I had only ever tried using it in CWL workflows, which was rejected by cwltool at the time. Keeping an eye out for use cases for this feature.
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Update 12/17:
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Tested run and recount with Lib303 dataset with various classes excluded or included. |
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This PR introduces functionality which allows users to specify classes that they want included or excluded in class DGE scatter plots. Inclusive/exclusive filtering is mutually exclusive (only one style can be chosen). Filtering takes place before subsetting features by P value, so it applies to non-differentially expressed features as well.
Additionally, the treatment condition is now listed first in the "ConditionA vs ConditionB" title of
scatter_by_dgeandscatter_by_dge_classplotsRemaining tasks:
Closes #262