Merge branch 'release/v1.1.0' into master

Author: pinin4fjords

scanpy-scripts-tests.bats

@@ -8,15 +8,19 @@ setup() {
     output_dir="${test_dir}/outputs"
     raw_matrix="${data_dir}/matrix.mtx"
     singlet_obs="${data_dir}/singlet_obs.txt"
+    batch_obs="${data_dir}/batch_obs.txt"
     read_opt="-x $data_dir --show-obj stdout"
     read_obj="${output_dir}/read.h5ad"
     filter_opt="--save-raw -p n_genes 200 2500 -p c:n_counts 0 50000 -p n_cells 3 inf -p pct_counts_mito 0 0.2 -c mito '!True' --show-obj stdout"
     filter_obj="${output_dir}/filter.h5ad"
+    test_clustering='louvain_k10_r0_5'
     scrublet_tsv="${output_dir}/scrublet.tsv"
     scrublet_png="${output_dir}/scrublet.png"
     scrublet_obj="${output_dir}/scrublet.h5ad"
+    scrublet_batched_obj="${output_dir}/scrublet_batched.h5ad"
     scrublet_simulate_obj="${output_dir}/scrublet_simulate.h5ad"
     scrublet_opt="--input-obj-sim ${scrublet_simulate_obj} --filter --export-table ${scrublet_tsv}"
+    scrublet_batched_opt="--filter --batch-key batch"
     norm_mtx="${output_dir}/norm"
     norm_opt="--save-layer filtered -t 10000 -l all -n after -X ${norm_mtx} --show-obj stdout"
     norm_obj="${output_dir}/norm.h5ad"
@@ -41,12 +45,11 @@ setup() {
     fdg_opt="--neighbors-key k10 --layout fr -E ${fdg_embed} --init-pos paga"
     fdg_obj="${output_dir}/fdg.h5ad"
     louvain_tsv="${output_dir}/louvain.tsv"
-    louvain_opt="-r 0.5,1 --neighbors-key k10 --key-added k10 --export-cluster ${louvain_tsv}"
+    louvain_opt="-r 0.1,0.5,1 --neighbors-key k10 --key-added k10 --export-cluster ${louvain_tsv}"
     louvain_obj="${output_dir}/louvain.h5ad"
     leiden_tsv="${output_dir}/leiden.tsv"
     leiden_opt="-r 0.3,0.7 --neighbors-key k10 --key-added k10 -F loom --loom-write-obsm-varm --export-cluster ${leiden_tsv}"
     leiden_obj="${output_dir}/leiden.loom"
-    test_clustering='louvain_k10_r0_5'
     diffexp_tsv="${output_dir}/diffexp.tsv"
     diffexp_opt="-g ${test_clustering} --reference rest --filter-params min_in_group_fraction:0.25,min_fold_change:1.5 --save ${diffexp_tsv}"
     diffexp_obj="${output_dir}/diffexp.h5ad"
@@ -126,14 +129,26 @@ setup() {
     [ -f "$singlet_obs" ]
 }
 
+@test "Make a batch variable" {
+
+    if [ "$resume" = 'true' ] && [ -f "$batch_obs" ]; then
+        skip "$singlet_obs exists"
+    fi
+
+    run rm -rf $batch_obs && echo -e "batch\n$(printf "%0.sbatch1\n" {1..1350})\n$(printf "%0.sbatch2\n" {1..1350})" > $batch_obs
+
+    [ "$status" -eq 0 ]
+    [ -f "$batch_obs" ]
+}
+
 # Read 10x dataset
 
 @test "Scanpy object creation from 10x" {
     if [ "$resume" = 'true' ] && [ -f "$read_obj" ]; then
         skip "$read_obj exists and resume is set to 'true'"
     fi
 
-    run rm -f $read_obj && eval "$scanpy read --extra-obs $singlet_obs $read_opt $read_obj"
+    run rm -f $read_obj && eval "paste -d $'\t' $singlet_obs $batch_obs > obs.txt && $scanpy read --extra-obs obs.txt $read_opt $read_obj"
 
     [ "$status" -eq 0 ]
     [ -f  "$read_obj" ]
@@ -218,6 +233,20 @@ setup() {
     [ -f  "$scrublet_png" ]
 }
 
+# Detect multiplets with Scrublet (batched)
+
+@test "Run Scrublet for multiplet detection (batched)" {
+    if [ "$resume" = 'true' ] && [ -f "$scrublet_batched_obj" ]; then
+        skip "$scrublet_batched_obj exists and resume is set to 'true'"
+    fi
+
+    run rm -f $scrublet_batched_obj && eval "$scanpy multiplet scrublet $scrublet_batched_opt $read_obj $scrublet_batched_obj"
+
+    [ "$status" -eq 0 ]
+    [ -f  "$scrublet_batched_obj" ]
+}
+
+
 # Regress out variables
 
 @test "Regress out unwanted variable" {

scanpy_scripts/cmd_options.py

@@ -1671,6 +1671,13 @@
     'scrublet': [
         *COMMON_OPTIONS['input'],
         *COMMON_OPTIONS['output'],
+        click.option(
+            '--batch-key', 'batch_key',
+            type=click.STRING,
+            default=None,
+            help='The name of the column in adata.obs that differentiates among '
+            'experiments/batches. Doublets will be detected in each batch separately.'
+        ),
         click.option(
             '--input-obj-sim', 'adata_sim',
             type=click.Path(exists=True, dir_okay=False),

scanpy_scripts/lib/_filter.py

@@ -66,8 +66,15 @@ def filter_anndata(
             logging.warning('`pct_counts_%s` exists, not overwriting '
                             'without --force-recalc', pt)
             pct_top.remove(pt)
+
+    # Calculate mito stats if we can, even if we're not filtering by them   
+
+    if 'mito' not in qc_vars and 'mito' in adata.var.keys():
+        qc_vars.append('mito')
+
     sc.pp.calculate_qc_metrics(
         adata, layer=layer, qc_vars=qc_vars, percent_top=pct_top, inplace=True)
+
     adata.obs['n_counts'] = adata.obs['total_counts']
     adata.obs['n_genes'] = adata.obs['n_genes_by_counts']
     adata.var['n_counts'] = adata.var['total_counts']

scanpy_scripts/lib/_scrublet.py

@@ -6,10 +6,12 @@
 import scanpy.external as sce
 import numpy as np
 from ..obj_utils import write_obs
+import anndata
+import pandas as pd
 
 # Wrapper for scrublet allowing text export and filtering
 
-def scrublet(adata, adata_sim=None, filter=False, export_table=None, **kwargs):
+def scrublet(adata, adata_sim=None, filter=False, batch_key=None, export_table=None, **kwargs):
     """
     Wrapper function for sce.pp.scrublet(), to allow filtering of resulting object
     """
@@ -19,8 +21,36 @@ def scrublet(adata, adata_sim=None, filter=False, export_table=None, **kwargs):
     if adata_sim:
         adata_sim = sc.read(adata_sim)
 
-    sce.pp.scrublet(adata, adata_sim=adata_sim, **kwargs)
+    # Scrublet shouldn't be run on multi-batch data, so we run the batches
+    # separately and copy the stats back to the input object
 
+    alldata = []
+    if batch_key is not None:
+        if batch_key not in adata.obs.keys():
+            raise ValueError('`batch_key` must be a column of .obs in the input annData object.')
+
+        batches = np.unique(adata.obs[batch_key])
+    
+        # Run Scrublet independently on batches and return just the
+        # scrublet-relevant parts of the objects to add to the input object
+
+        def get_adata_scrub_parts(ad):
+            return {'obs': ad.obs, 'uns': ad.uns['scrublet']}
+
+        scrubbed = [ get_adata_scrub_parts(sce.pp.scrublet(adata[adata.obs[batch_key] == batch,], adata_sim=adata_sim, copy = True, **kwargs)) for batch in batches ] 
+        scrubbed_obs = pd.concat([ scrub['obs'] for scrub in scrubbed])        
+
+        # Now reset the obs to get the scrublet scores
+        
+        adata.obs = scrubbed_obs.loc[adata.obs_names.values]
+
+        # Save the .uns from each batch separately
+    
+        adata.uns['scrublet'] = dict(zip(batches, [ scrub['uns'] for scrub in scrubbed ]))
+
+    else:
+        sce.pp.scrublet(adata, adata_sim=adata_sim, **kwargs)
+    
     # Do any export before optional filtering
 
     if export_table:

setup.py

@@ -5,7 +5,7 @@
 
 setup(
     name='scanpy-scripts',
-    version='1.0.1',
+    version='1.1.0',
     author='nh3',
     author_email='[email protected]',
     description='Scripts for using scanpy from the command line',