mirror of
https://github.com/chanzuckerberg/cellxgene.git
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b90447c387
* first flatbuffer schema * do not lint auto-generated files * add flatbuffers package * add flatbuffer module * wire up /data/X/T route * use flatbuffers for matrix data fetc * clarity and comments * add flatbuffer layout route * clean up obsolete code * fix tests * move flake8 config to setup.cfg * add comments * lint * rework layout routes for fbs * add more type support to fbs * lint * add flatbuffer support for annotations * function name improvements * fix botched merge with master * remove unused import * route cleanup for flatbuffers * rename function for clarity * add missing globals to Jest tests * fix client JS tests * fix routes for Python tests * comments for clarity * non-finite floating point hardening * more non-finite number handling * lint * fix tests for summarizeAnnotations * harden diffexp calculation against FP errors * cleanup unused code * lint * add encoding tests for flatbuffers * application type specified as strings * fix spelling error * improve variable names * add note about documentation gap * rename FBS DataFrame to Matrix
123 lines
4.5 KiB
Python
123 lines
4.5 KiB
Python
import numpy as np
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from scipy import sparse, stats
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# Convenience function which handles sparse data
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def _mean_var_n(X):
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"""
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Two-pass variance calculation. Numerically (more) stable
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than naive methods (and same method used by numpy.var())
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https://en.wikipedia.org/wiki/Algorithms_for_calculating_variance#Two-pass
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"""
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# fp_err_occurred is a flag indicating that a floating point error
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# occured somewhere in our compute. Used to trigger non-finite
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# number handling.
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fp_err_occurred = False
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def fp_err_set(err, flag):
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nonlocal fp_err_occurred
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fp_err_occurred = True
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with np.errstate(divide="call", invalid="call", call=fp_err_set):
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n = X.shape[0]
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if sparse.issparse(X):
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mean = X.mean(axis=0).A1
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dfm = X - mean
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sumsq = np.sum(np.multiply(dfm, dfm), axis=0).A1
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v = sumsq / (n - 1)
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else:
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mean = X.mean(axis=0)
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dfm = X - mean
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sumsq = np.sum(np.multiply(dfm, dfm), axis=0)
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v = sumsq / (n - 1)
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if fp_err_occurred:
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mean[np.isfinite(mean) == False] = 0 # noqa: E712
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v[np.isfinite(v) == False] = 0 # noqa: E712
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return mean, v, n
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def diffexp_ttest(adata, maskA, maskB, top_n=8, diffexp_lfc_cutoff=0.01):
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"""
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Return differential expression statistics for top N variables.
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Algorithm:
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- compute log fold change (log2(meanA/meanB))
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- compute Welch's t-test statistic and pvalue (w/ Bonferroni correction)
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- return top N abs(logfoldchange) where lfc > diffexp_lfc_cutoff
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If there are not N which meet criteria, augment by removing the logfoldchange
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threshold requirement.
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Notes on alogrithm:
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- Welch's ttest provides basic statistics test.
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https://en.wikipedia.org/wiki/Welch%27s_t-test
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- p-values adjusted with Bonferroni correction.
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https://en.wikipedia.org/wiki/Bonferroni_correction
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:param adata: anndata dataframe
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:param maskA: observation selection mask for set 1
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:param maskB: observation selection mask for set 2
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:param top_n: number of variables to return stats for
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:param diffexp_lfc_cutoff: minimum
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:return: for top N genes, [ varindex, logfoldchange, pval, pval_adj ]
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"""
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if top_n > adata.n_obs:
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top_n = adata.n_obs
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# mean, variance, N - calculate for both selections
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meanA, vA, nA = _mean_var_n(adata._X[maskA])
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meanB, vB, nB = _mean_var_n(adata._X[maskB])
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# variance / N
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vnA = vA / min(nA, nB) # overestimate variance, would normally be nA
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vnB = vB / min(nA, nB) # overestimate variance, would normally be nB
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sum_vn = vnA + vnB
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# degrees of freedom for Welch's t-test
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with np.errstate(divide="ignore", invalid="ignore"):
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dof = sum_vn ** 2 / (vnA ** 2 / (nA - 1) + vnB ** 2 / (nB - 1))
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dof[np.isnan(dof)] = 1
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# Welch's t-test score calculation
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with np.errstate(divide="ignore", invalid="ignore"):
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tscores = (meanA - meanB) / np.sqrt(sum_vn)
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tscores[np.isnan(tscores)] = 0
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# p-value
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pvals = stats.t.sf(np.abs(tscores), dof) * 2
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pvals_adj = pvals * adata._X.shape[1]
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pvals_adj[pvals_adj > 1] = 1 # cap adjusted p-value at 1
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# logfoldchanges: log2(meanA / meanB)
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logfoldchanges = np.log2(np.abs((meanA + 1e-9) / (meanB + 1e-9)))
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# find all with lfc > cutoff
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lfc_above_cutoff_idx = np.nonzero(np.abs(logfoldchanges) > diffexp_lfc_cutoff)[0]
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stats_to_sort = np.abs(tscores)
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# derive sort order
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if lfc_above_cutoff_idx.shape[0] > top_n:
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# partition top N
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rel_t_partition = np.argpartition(stats_to_sort[lfc_above_cutoff_idx], -top_n)[-top_n:]
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t_partition = lfc_above_cutoff_idx[rel_t_partition]
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# sort the top N partition
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rel_sort_order = np.argsort(stats_to_sort[t_partition])[::-1]
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sort_order = t_partition[rel_sort_order]
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else:
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# partition and sort top N, ignoring lfc cutoff
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partition = np.argpartition(stats_to_sort, -top_n)[-top_n:]
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rel_sort_order = np.argsort(stats_to_sort[partition])[::-1]
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indices = np.indices(stats_to_sort.shape)[0]
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sort_order = indices[partition][rel_sort_order]
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# top n slice based upon sort order
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logfoldchanges_top_n = logfoldchanges[sort_order]
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pvals_top_n = pvals[sort_order]
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pvals_adj_top_n = pvals_adj[sort_order]
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# varIndex, logfoldchange, pval, pval_adj
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result = [[sort_order[i], logfoldchanges_top_n[i], pvals_top_n[i], pvals_adj_top_n[i]] for i in range(top_n)]
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return result
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