Add plot_bcv()#1007
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LuisHeinzlmeier
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Jun 3, 2026
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Zethson
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Jun 3, 2026
| self.fit = fit | ||
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| @_doc_params(common_plot_args=doc_common_plot_args) | ||
| def plot_bcv( # pragma: no cover # noqa: D417 |
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This is only designed for edger now, right? But it should also work with statsmodels or pydeseq2. Like ideally, I'd like to completely phase out the edger support at some point in the future.
| >>> adata.layers["counts"] = adata.X.copy() | ||
| >>> pdata = dc.pp.pseudobulk(adata, sample_col="Patient", groups_col="Cluster", layer="counts", mode="sum") | ||
| >>> dc.pp.filter_samples(pdata, inplace=True) | ||
| >>> edgr = pt.tl.EdgeR(pdata, design="~Efficacy+Treatment") |
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| ro.globalenv["fit"] = fit | ||
| self.fit = fit | ||
| self.dge = dge |
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plot_bcv()_prepare_dge()to be able to runplot_bcv()before.fit()without calculating normalization factors and estimating dispersions twice_ensure_deps()to prevent repetitive imports and code