Split out the local backend (#2052)

This splits the backend into two parts: the local backend for desktop cellxgene and the AWS backend for hosted cellxgene. The local backend is in local_server while the hosted remains in server. The general idea is to copy everything from server to local_server, pull unneeded stuff out of local_server, and keep server as-is for this PR. Not touching server means all the infra and deployment code will continue working just as it did before so we can make those changes incrementally.
2026-10-02 21:28:11 +08:00 · 2021-02-18 12:58:22 -08:00
parent 036b5f8c0f
commit fb61bd6e9c
153 changed files with 14027 additions and 46 deletions
@@ -0,0 +1,134 @@
+import numpy as np
+from scipy import sparse, stats
+
+
+def diffexp_ttest(adaptor, maskA, maskB, top_n=8, diffexp_lfc_cutoff=0.01):
+    """
+    Return differential expression statistics for top N variables.
+
+    Algorithm:
+    - compute log fold change (log2(meanA/meanB))
+    - compute Welch's t-test statistic and pvalue (w/ Bonferroni correction)
+    - return top N abs(logfoldchange) where lfc > diffexp_lfc_cutoff
+
+    If there are not N which meet criteria, augment by removing the logfoldchange
+    threshold requirement.
+
+    Notes on alogrithm:
+    - Welch's ttest provides basic statistics test.
+      https://en.wikipedia.org/wiki/Welch%27s_t-test
+    - p-values adjusted with Bonferroni correction.
+      https://en.wikipedia.org/wiki/Bonferroni_correction
+
+    :param adaptor: DataAdaptor instance
+    :param maskA: observation selection mask for set 1
+    :param maskB: observation selection mask for set 2
+    :param top_n: number of variables to return stats for
+    :param diffexp_lfc_cutoff: minimum
+    :return:  for top N genes, [ varindex, logfoldchange, pval, pval_adj ]
+    """
+
+    dataA = adaptor.get_X_array(maskA, None)
+    dataB = adaptor.get_X_array(maskB, None)
+
+    # mean, variance, N - calculate for both selections
+    meanA, vA, nA = mean_var_n(dataA)
+    meanB, vB, nB = mean_var_n(dataB)
+    res = diffexp_ttest_from_mean_var(meanA, vA, nA, meanB, vB, nB, top_n, diffexp_lfc_cutoff)
+
+    return res
+
+
+def diffexp_ttest_from_mean_var(meanA, varA, nA, meanB, varB, nB, top_n, diffexp_lfc_cutoff):
+    n_var = meanA.shape[0]
+    top_n = min(top_n, n_var)
+
+    # variance / N
+    vnA = varA / min(nA, nB)  # overestimate variance, would normally be nA
+    vnB = varB / min(nA, nB)  # overestimate variance, would normally be nB
+    sum_vn = vnA + vnB
+
+    # degrees of freedom for Welch's t-test
+    with np.errstate(divide="ignore", invalid="ignore"):
+        dof = sum_vn ** 2 / (vnA ** 2 / (nA - 1) + vnB ** 2 / (nB - 1))
+    dof[np.isnan(dof)] = 1
+
+    # Welch's t-test score calculation
+    with np.errstate(divide="ignore", invalid="ignore"):
+        tscores = (meanA - meanB) / np.sqrt(sum_vn)
+    tscores[np.isnan(tscores)] = 0
+
+    # p-value
+    pvals = stats.t.sf(np.abs(tscores), dof) * 2
+    pvals_adj = pvals * n_var
+    pvals_adj[pvals_adj > 1] = 1  # cap adjusted p-value at 1
+
+    # logfoldchanges: log2(meanA / meanB)
+    logfoldchanges = np.log2(np.abs((meanA + 1e-9) / (meanB + 1e-9)))
+
+    # find all with lfc > cutoff
+    lfc_above_cutoff_idx = np.nonzero(np.abs(logfoldchanges) > diffexp_lfc_cutoff)[0]
+    stats_to_sort = np.abs(tscores)
+
+    # derive sort order
+    if lfc_above_cutoff_idx.shape[0] > top_n:
+        # partition top N
+        rel_t_partition = np.argpartition(stats_to_sort[lfc_above_cutoff_idx], -top_n)[-top_n:]
+        t_partition = lfc_above_cutoff_idx[rel_t_partition]
+        # sort the top N partition
+        rel_sort_order = np.argsort(stats_to_sort[t_partition])[::-1]
+        sort_order = t_partition[rel_sort_order]
+    else:
+        # partition and sort top N, ignoring lfc cutoff
+        partition = np.argpartition(stats_to_sort, -top_n)[-top_n:]
+        rel_sort_order = np.argsort(stats_to_sort[partition])[::-1]
+        indices = np.indices(stats_to_sort.shape)[0]
+        sort_order = indices[partition][rel_sort_order]
+
+    # top n slice based upon sort order
+    logfoldchanges_top_n = logfoldchanges[sort_order]
+    pvals_top_n = pvals[sort_order]
+    pvals_adj_top_n = pvals_adj[sort_order]
+
+    # varIndex, logfoldchange, pval, pval_adj
+    result = [[sort_order[i], logfoldchanges_top_n[i], pvals_top_n[i], pvals_adj_top_n[i]] for i in range(top_n)]
+    return result
+
+
+# Convenience function which handles sparse data
+def mean_var_n(X):
+    """
+    Two-pass variance calculation.  Numerically (more) stable
+    than naive methods (and same method used by numpy.var())
+    https://en.wikipedia.org/wiki/Algorithms_for_calculating_variance#Two-pass
+    """
+    # fp_err_occurred is a flag indicating that a floating point error
+    # occured somewhere in our compute.  Used to trigger non-finite
+    # number handling.
+    fp_err_occurred = False
+
+    def fp_err_set(err, flag):
+        nonlocal fp_err_occurred
+        fp_err_occurred = True
+
+    with np.errstate(divide="call", invalid="call", call=fp_err_set):
+        n = X.shape[0]
+        if sparse.issparse(X):
+            mean = X.mean(axis=0).A1
+            dfm = X - mean
+            sumsq = np.sum(np.multiply(dfm, dfm), axis=0).A1
+            v = sumsq / (n - 1)
+        else:
+            mean = X.mean(axis=0)
+            dfm = X - mean
+            sumsq = np.sum(np.multiply(dfm, dfm), axis=0)
+            v = sumsq / (n - 1)
+
+    if fp_err_occurred:
+        mean[np.isfinite(mean) == False] = 0  # noqa: E712
+        v[np.isfinite(v) == False] = 0  # noqa: E712
+    else:
+        mean[np.isnan(mean)] = 0
+        v[np.isnan(v)] = 0
+
+    return mean, v, n
@@ -0,0 +1,53 @@
+import importlib
+import numpy as np
+
+"""
+Wrapper for various scanpy modules.  Will raise NotImplementedError if the scanpy
+module is not installed/available
+"""
+
+
+def get_scanpy_module():
+    try:
+        sc = importlib.import_module("scanpy")
+        # Future: we could enforce versions here, eg, lookat sc.__version__
+        return sc
+    except ModuleNotFoundError as e:
+        raise NotImplementedError("Please install scanpy to enable UMAP re-embedding") from e
+    except Exception as e:
+        # will capture other ImportError corner cases
+        raise NotImplementedError() from e
+
+
+def scanpy_umap(adata, obs_mask=None, pca_options={}, neighbors_options={}, umap_options={}):
+    """
+    Given adata and an obs mask, return a new embedding for adata[obs_mask, :]
+    as an ndarray of shape (len(obs_mask), N), where N>=2.
+
+    Do NOT mutate adata.
+    """
+
+    # backed mode is incompatible with the current implementation
+    if adata.isbacked:
+        raise NotImplementedError("Backed mode is incompatible with re-embedding")
+
+    # safely get scanpy module, which may not be present.
+    sc = get_scanpy_module()
+
+    # https://github.com/theislab/anndata/issues/311
+    obs_mask = slice(None) if obs_mask is None else obs_mask
+    adata = adata[obs_mask, :].copy()
+
+    for k in list(adata.obsm.keys()):
+        del adata.obsm[k]
+    for k in list(adata.uns.keys()):
+        del adata.uns[k]
+
+    sc.pp.pca(adata, zero_center=None, n_comps=min(adata.n_vars - 1, 50), **pca_options)
+    sc.pp.neighbors(adata, **neighbors_options)
+    sc.tl.umap(adata, **umap_options)
+
+    umap = adata.obsm["X_umap"]
+    result = np.full((obs_mask.shape[0], umap.shape[1]), np.NaN)
+    result[obs_mask] = umap
+    return result