Cell subsampling using TopACeDo¶
[1]:
%load_ext autotime
%config InlineBackend.figure_format = 'retina'
import scarf
scarf.__version__
[1]:
'0.7.8'
time: 1.54 s (started: 2021-08-22 17:57:10 +00:00)
1) Installing dependencies¶
We need to install the TopACeDo algorithm to perform subsampling
[2]:
!pip install git+https://github.com/fraenkel-lab/pcst_fast.git@deb3236cc26ee9fee77d5af40fac3f12bb753850
!pip install -U topacedo
Collecting git+https://github.com/fraenkel-lab/pcst_fast.git@deb3236cc26ee9fee77d5af40fac3f12bb753850
Cloning https://github.com/fraenkel-lab/pcst_fast.git (to revision deb3236cc26ee9fee77d5af40fac3f12bb753850) to /tmp/pip-req-build-kwah0_84
Running command git clone -q https://github.com/fraenkel-lab/pcst_fast.git /tmp/pip-req-build-kwah0_84
Running command git rev-parse -q --verify 'sha^deb3236cc26ee9fee77d5af40fac3f12bb753850'
Running command git fetch -q https://github.com/fraenkel-lab/pcst_fast.git deb3236cc26ee9fee77d5af40fac3f12bb753850
Running command git checkout -q deb3236cc26ee9fee77d5af40fac3f12bb753850
Resolved https://github.com/fraenkel-lab/pcst_fast.git to commit deb3236cc26ee9fee77d5af40fac3f12bb753850
Requirement already satisfied: pybind11>=2.1.0 in /home/docs/checkouts/readthedocs.org/user_builds/scarf/envs/0.7.8/lib/python3.8/site-packages (from pcst-fast==1.0.7) (2.7.1)
Building wheels for collected packages: pcst-fast
Building wheel for pcst-fast (setup.py) ... - \ | / - \ done
Created wheel for pcst-fast: filename=pcst_fast-1.0.7-cp38-cp38-linux_x86_64.whl size=840708 sha256=1f65bb2df5e208a4c84487443a39f61a68859676b362347b7421b5546ceab15d
Stored in directory: /home/docs/.cache/pip/wheels/48/f1/74/6bb2e9cc262228dbdc63916ec60f0717574b5f633b6ee30b0a
Successfully built pcst-fast
Installing collected packages: pcst-fast
Successfully installed pcst-fast-1.0.7
Requirement already satisfied: topacedo in /home/docs/checkouts/readthedocs.org/user_builds/scarf/envs/0.7.8/lib/python3.8/site-packages (0.2.7)
time: 21.6 s (started: 2021-08-22 17:57:12 +00:00)
2) Fetching pre-processed data¶
[3]:
# Loading preanalyzed dataset that was processed in the `basic_tutorial` vignette
scarf.fetch_dataset('tenx_5K_pbmc_rnaseq', as_zarr=True, save_path='scarf_datasets')
INFO: Download started...
--2021-08-22 17:57:39-- https://files.de-1.osf.io/v1/resources/zeupv/providers/osfstorage/6096d5685533b405bfe1eeb3
Resolving files.de-1.osf.io (files.de-1.osf.io)... 35.186.249.111
Connecting to files.de-1.osf.io (files.de-1.osf.io)|35.186.249.111|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://storage.googleapis.com/cos-osf-prod-files-de-1/1ef8b465325d04f0b87ed06fe7813ec6698d1a9a45e3511e885ae45e732f9bb8?response-content-disposition=attachment%3B%20filename%3D%22data.zarr.tar.gz%22%3B%20filename%2A%3DUTF-8%27%27data.zarr.tar.gz&GoogleAccessId=files-de-1%40cos-osf-prod.iam.gserviceaccount.com&Expires=1629655121&Signature=azppnAgIYfK4mvm3snLSwtr6dn0PQAOsAX%2Bl7Ux4L9LP70jCjhIQLW7Dx7b2gEw347fdzqVdop4QanPbM9IfvGx9cgJ0buC6XRVxKJPYOsGno2mmDDtCxXI5gBQvENukwA57m6zyQyNEtUUJ2%2BH8qH8JiFB6B%2BiUIWmZlWo1Zc6AUnMpeTjrKJCI5dojU%2ByJwObEne96EeRtdfh2pOBdWxwv8AMuSsGr%2FwGnBzBM2mQZvkJzA9cCgYo6BC4jmI9OTvFqsr2PniHlPDtZdDFQY59IxGJuiN5bOkwBma%2Fwup7WJs9muaNudM7G42BH5junU6Eu%2B9SAbv8eIjltdcdGvg%3D%3D [following]
--2021-08-22 17:57:41-- https://storage.googleapis.com/cos-osf-prod-files-de-1/1ef8b465325d04f0b87ed06fe7813ec6698d1a9a45e3511e885ae45e732f9bb8?response-content-disposition=attachment%3B%20filename%3D%22data.zarr.tar.gz%22%3B%20filename%2A%3DUTF-8%27%27data.zarr.tar.gz&GoogleAccessId=files-de-1%40cos-osf-prod.iam.gserviceaccount.com&Expires=1629655121&Signature=azppnAgIYfK4mvm3snLSwtr6dn0PQAOsAX%2Bl7Ux4L9LP70jCjhIQLW7Dx7b2gEw347fdzqVdop4QanPbM9IfvGx9cgJ0buC6XRVxKJPYOsGno2mmDDtCxXI5gBQvENukwA57m6zyQyNEtUUJ2%2BH8qH8JiFB6B%2BiUIWmZlWo1Zc6AUnMpeTjrKJCI5dojU%2ByJwObEne96EeRtdfh2pOBdWxwv8AMuSsGr%2FwGnBzBM2mQZvkJzA9cCgYo6BC4jmI9OTvFqsr2PniHlPDtZdDFQY59IxGJuiN5bOkwBma%2Fwup7WJs9muaNudM7G42BH5junU6Eu%2B9SAbv8eIjltdcdGvg%3D%3D
Resolving storage.googleapis.com (storage.googleapis.com)... 172.217.4.48, 172.217.4.80, 172.217.4.208, ...
Connecting to storage.googleapis.com (storage.googleapis.com)|172.217.4.48|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 31491651 (30M) [application/octet-stream]
Saving to: ‘scarf_datasets/tenx_5K_pbmc_rnaseq/data.zarr.tar.gz’
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11500K .......... .......... .......... .......... .......... 37% 103M 1s
11550K .......... .......... .......... .......... .......... 37% 235M 1s
11600K .......... .......... .......... .......... .......... 37% 145M 1s
11650K .......... .......... .......... .......... .......... 38% 226M 1s
11700K .......... .......... .......... .......... .......... 38% 3.50M 1s
11750K .......... .......... .......... .......... .......... 38% 12.6M 1s
11800K .......... .......... .......... .......... .......... 38% 53.9M 1s
11850K .......... .......... .......... .......... .......... 38% 87.5M 1s
11900K .......... .......... .......... .......... .......... 38% 127M 1s
11950K .......... .......... .......... .......... .......... 39% 245M 1s
12000K .......... .......... .......... .......... .......... 39% 7.22M 1s
12050K .......... .......... .......... .......... .......... 39% 156M 1s
12100K .......... .......... .......... .......... .......... 39% 168M 1s
12150K .......... .......... .......... .......... .......... 39% 15.0M 1s
12200K .......... .......... .......... .......... .......... 39% 37.4M 1s
12250K .......... .......... .......... .......... .......... 39% 126M 1s
12300K .......... .......... .......... .......... .......... 40% 129M 1s
12350K .......... .......... .......... .......... .......... 40% 15.3M 1s
12400K .......... .......... .......... .......... .......... 40% 137M 1s
12450K .......... .......... .......... .......... .......... 40% 56.7M 1s
12500K .......... .......... .......... .......... .......... 40% 17.6M 1s
12550K .......... .......... .......... .......... .......... 40% 74.9M 1s
12600K .......... .......... .......... .......... .......... 41% 152M 1s
12650K .......... .......... .......... .......... .......... 41% 141M 1s
12700K .......... .......... .......... .......... .......... 41% 149M 1s
12750K .......... .......... .......... .......... .......... 41% 15.8M 1s
12800K .......... .......... .......... .......... .......... 41% 144M 1s
12850K .......... .......... .......... .......... .......... 41% 150M 1s
12900K .......... .......... .......... .......... .......... 42% 152M 1s
12950K .......... .......... .......... .......... .......... 42% 16.0M 1s
13000K .......... .......... .......... .......... .......... 42% 136M 1s
13050K .......... .......... .......... .......... .......... 42% 38.2M 1s
13100K .......... .......... .......... .......... .......... 42% 41.4M 1s
13150K .......... .......... .......... .......... .......... 42% 124M 1s
13200K .......... .......... .......... .......... .......... 43% 153M 1s
13250K .......... .......... .......... .......... .......... 43% 145M 1s
13300K .......... .......... .......... .......... .......... 43% 156M 1s
13350K .......... .......... .......... .......... .......... 43% 7.77M 1s
13400K .......... .......... .......... .......... .......... 43% 16.4M 1s
13450K .......... .......... .......... .......... .......... 43% 81.4M 1s
13500K .......... .......... .......... .......... .......... 44% 213M 1s
13550K .......... .......... .......... .......... .......... 44% 175M 1s
13600K .......... .......... .......... .......... .......... 44% 221M 1s
13650K .......... .......... .......... .......... .......... 44% 218M 1s
13700K .......... .......... .......... .......... .......... 44% 213M 1s
13750K .......... .......... .......... .......... .......... 44% 192M 1s
13800K .......... .......... .......... .......... .......... 45% 140M 1s
13850K .......... .......... .......... .......... .......... 45% 109M 1s
13900K .......... .......... .......... .......... .......... 45% 214M 1s
13950K .......... .......... .......... .......... .......... 45% 123M 1s
14000K .......... .......... .......... .......... .......... 45% 213M 1s
14050K .......... .......... .......... .......... .......... 45% 8.02M 1s
14100K .......... .......... .......... .......... .......... 46% 6.44M 1s
14150K .......... .......... .......... .......... .......... 46% 18.5M 1s
14200K .......... .......... .......... .......... .......... 46% 81.1M 1s
14250K .......... .......... .......... .......... .......... 46% 156M 1s
14300K .......... .......... .......... .......... .......... 46% 24.6M 1s
14350K .......... .......... .......... .......... .......... 46% 72.8M 1s
14400K .......... .......... .......... .......... .......... 46% 144M 1s
14450K .......... .......... .......... .......... .......... 47% 97.8M 1s
14500K .......... .......... .......... .......... .......... 47% 22.1M 1s
14550K .......... .......... .......... .......... .......... 47% 22.7M 1s
14600K .......... .......... .......... .......... .......... 47% 151M 1s
14650K .......... .......... .......... .......... .......... 47% 146M 1s
14700K .......... .......... .......... .......... .......... 47% 154M 1s
14750K .......... .......... .......... .......... .......... 48% 129M 1s
14800K .......... .......... .......... .......... .......... 48% 133M 1s
14850K .......... .......... .......... .......... .......... 48% 138M 1s
14900K .......... .......... .......... .......... .......... 48% 152M 1s
14950K .......... .......... .......... .......... .......... 48% 133M 1s
15000K .......... .......... .......... .......... .......... 48% 144M 1s
15050K .......... .......... .......... .......... .......... 49% 152M 1s
15100K .......... .......... .......... .......... .......... 49% 23.2M 1s
15150K .......... .......... .......... .......... .......... 49% 14.9M 1s
15200K .......... .......... .......... .......... .......... 49% 20.1M 1s
15250K .......... .......... .......... .......... .......... 49% 89.6M 1s
15300K .......... .......... .......... .......... .......... 49% 159M 1s
15350K .......... .......... .......... .......... .......... 50% 134M 1s
15400K .......... .......... .......... .......... .......... 50% 144M 1s
15450K .......... .......... .......... .......... .......... 50% 162M 1s
15500K .......... .......... .......... .......... .......... 50% 145M 1s
15550K .......... .......... .......... .......... .......... 50% 130M 1s
15600K .......... .......... .......... .......... .......... 50% 149M 1s
15650K .......... .......... .......... .......... .......... 51% 18.5M 1s
15700K .......... .......... .......... .......... .......... 51% 17.3M 1s
15750K .......... .......... .......... .......... .......... 51% 40.8M 1s
15800K .......... .......... .......... .......... .......... 51% 148M 1s
15850K .......... .......... .......... .......... .......... 51% 148M 1s
15900K .......... .......... .......... .......... .......... 51% 144M 1s
15950K .......... .......... .......... .......... .......... 52% 129M 1s
16000K .......... .......... .......... .......... .......... 52% 161M 1s
16050K .......... .......... .......... .......... .......... 52% 140M 1s
16100K .......... .......... .......... .......... .......... 52% 147M 1s
16150K .......... .......... .......... .......... .......... 52% 136M 1s
16200K .......... .......... .......... .......... .......... 52% 141M 1s
16250K .......... .......... .......... .......... .......... 53% 154M 1s
16300K .......... .......... .......... .......... .......... 53% 161M 1s
16350K .......... .......... .......... .......... .......... 53% 335K 1s
16400K .......... .......... .......... .......... .......... 53% 11.0M 1s
16450K .......... .......... .......... .......... .......... 53% 6.42M 1s
16500K .......... .......... .......... .......... .......... 53% 17.6M 1s
16550K .......... .......... .......... .......... .......... 53% 18.3M 1s
16600K .......... .......... .......... .......... .......... 54% 32.7M 1s
16650K .......... .......... .......... .......... .......... 54% 230M 1s
16700K .......... .......... .......... .......... .......... 54% 210M 1s
16750K .......... .......... .......... .......... .......... 54% 199M 1s
16800K .......... .......... .......... .......... .......... 54% 186M 1s
16850K .......... .......... .......... .......... .......... 54% 222M 1s
16900K .......... .......... .......... .......... .......... 55% 225M 1s
16950K .......... .......... .......... .......... .......... 55% 237M 1s
17000K .......... .......... .......... .......... .......... 55% 214M 1s
17050K .......... .......... .......... .......... .......... 55% 223M 1s
17100K .......... .......... .......... .......... .......... 55% 236M 1s
17150K .......... .......... .......... .......... .......... 55% 4.55M 1s
17200K .......... .......... .......... .......... .......... 56% 15.7M 1s
17250K .......... .......... .......... .......... .......... 56% 17.3M 1s
17300K .......... .......... .......... .......... .......... 56% 24.9M 1s
17350K .......... .......... .......... .......... .......... 56% 214M 1s
17400K .......... .......... .......... .......... .......... 56% 207M 1s
17450K .......... .......... .......... .......... .......... 56% 212M 1s
17500K .......... .......... .......... .......... .......... 57% 220M 1s
17550K .......... .......... .......... .......... .......... 57% 236M 1s
17600K .......... .......... .......... .......... .......... 57% 189M 1s
17650K .......... .......... .......... .......... .......... 57% 17.6M 1s
17700K .......... .......... .......... .......... .......... 57% 18.2M 1s
17750K .......... .......... .......... .......... .......... 57% 29.1M 1s
17800K .......... .......... .......... .......... .......... 58% 208M 1s
17850K .......... .......... .......... .......... .......... 58% 199M 1s
17900K .......... .......... .......... .......... .......... 58% 236M 1s
17950K .......... .......... .......... .......... .......... 58% 243M 1s
18000K .......... .......... .......... .......... .......... 58% 161M 1s
18050K .......... .......... .......... .......... .......... 58% 230M 1s
18100K .......... .......... .......... .......... .......... 59% 217M 1s
18150K .......... .......... .......... .......... .......... 59% 239M 1s
18200K .......... .......... .......... .......... .......... 59% 217M 1s
18250K .......... .......... .......... .......... .......... 59% 230M 1s
18300K .......... .......... .......... .......... .......... 59% 235M 1s
18350K .......... .......... .......... .......... .......... 59% 225M 1s
18400K .......... .......... .......... .......... .......... 59% 186M 1s
18450K .......... .......... .......... .......... .......... 60% 240M 1s
18500K .......... .......... .......... .......... .......... 60% 228M 1s
18550K .......... .......... .......... .......... .......... 60% 237M 1s
18600K .......... .......... .......... .......... .......... 60% 217M 1s
18650K .......... .......... .......... .......... .......... 60% 218M 1s
18700K .......... .......... .......... .......... .......... 60% 243M 1s
18750K .......... .......... .......... .......... .......... 61% 230M 1s
18800K .......... .......... .......... .......... .......... 61% 195M 1s
18850K .......... .......... .......... .......... .......... 61% 241M 1s
18900K .......... .......... .......... .......... .......... 61% 118M 1s
18950K .......... .......... .......... .......... .......... 61% 190M 1s
19000K .......... .......... .......... .......... .......... 61% 143M 1s
19050K .......... .......... .......... .......... .......... 62% 163M 1s
19100K .......... .......... .......... .......... .......... 62% 167M 1s
19150K .......... .......... .......... .......... .......... 62% 169M 1s
19200K .......... .......... .......... .......... .......... 62% 133M 1s
19250K .......... .......... .......... .......... .......... 62% 164M 1s
19300K .......... .......... .......... .......... .......... 62% 23.2M 1s
19350K .......... .......... .......... .......... .......... 63% 38.6M 1s
19400K .......... .......... .......... .......... .......... 63% 153M 1s
19450K .......... .......... .......... .......... .......... 63% 150M 1s
19500K .......... .......... .......... .......... .......... 63% 205M 1s
19550K .......... .......... .......... .......... .......... 63% 164M 1s
19600K .......... .......... .......... .......... .......... 63% 136M 1s
19650K .......... .......... .......... .......... .......... 64% 159M 1s
19700K .......... .......... .......... .......... .......... 64% 160M 1s
19750K .......... .......... .......... .......... .......... 64% 14.1M 1s
19800K .......... .......... .......... .......... .......... 64% 139M 1s
19850K .......... .......... .......... .......... .......... 64% 5.89M 1s
19900K .......... .......... .......... .......... .......... 64% 202M 1s
19950K .......... .......... .......... .......... .......... 65% 207M 1s
20000K .......... .......... .......... .......... .......... 65% 199M 1s
20050K .......... .......... .......... .......... .......... 65% 232M 1s
20100K .......... .......... .......... .......... .......... 65% 196M 1s
20150K .......... .......... .......... .......... .......... 65% 237M 1s
20200K .......... .......... .......... .......... .......... 65% 214M 1s
20250K .......... .......... .......... .......... .......... 66% 210M 1s
20300K .......... .......... .......... .......... .......... 66% 241M 1s
20350K .......... .......... .......... .......... .......... 66% 243M 1s
20400K .......... .......... .......... .......... .......... 66% 178M 0s
20450K .......... .......... .......... .......... .......... 66% 232M 0s
20500K .......... .......... .......... .......... .......... 66% 240M 0s
20550K .......... .......... .......... .......... .......... 66% 226M 0s
20600K .......... .......... .......... .......... .......... 67% 220M 0s
20650K .......... .......... .......... .......... .......... 67% 196M 0s
20700K .......... .......... .......... .......... .......... 67% 227M 0s
20750K .......... .......... .......... .......... .......... 67% 217M 0s
20800K .......... .......... .......... .......... .......... 67% 189M 0s
20850K .......... .......... .......... .......... .......... 67% 230M 0s
20900K .......... .......... .......... .......... .......... 68% 43.2M 0s
20950K .......... .......... .......... .......... .......... 68% 15.6M 0s
21000K .......... .......... .......... .......... .......... 68% 19.4M 0s
21050K .......... .......... .......... .......... .......... 68% 121M 0s
21100K .......... .......... .......... .......... .......... 68% 220M 0s
21150K .......... .......... .......... .......... .......... 68% 230M 0s
21200K .......... .......... .......... .......... .......... 69% 165M 0s
21250K .......... .......... .......... .......... .......... 69% 235M 0s
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21400K .......... .......... .......... .......... .......... 69% 216M 0s
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21500K .......... .......... .......... .......... .......... 70% 220M 0s
21550K .......... .......... .......... .......... .......... 70% 227M 0s
21600K .......... .......... .......... .......... .......... 70% 193M 0s
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21700K .......... .......... .......... .......... .......... 70% 226M 0s
21750K .......... .......... .......... .......... .......... 70% 5.23M 0s
21800K .......... .......... .......... .......... .......... 71% 135M 0s
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21950K .......... .......... .......... .......... .......... 71% 168M 0s
22000K .......... .......... .......... .......... .......... 71% 189M 0s
22050K .......... .......... .......... .......... .......... 71% 220M 0s
22100K .......... .......... .......... .......... .......... 72% 145M 0s
22150K .......... .......... .......... .......... .......... 72% 236M 0s
22200K .......... .......... .......... .......... .......... 72% 107M 0s
22250K .......... .......... .......... .......... .......... 72% 218M 0s
22300K .......... .......... .......... .......... .......... 72% 227M 0s
22350K .......... .......... .......... .......... .......... 72% 224M 0s
22400K .......... .......... .......... .......... .......... 72% 192M 0s
22450K .......... .......... .......... .......... .......... 73% 6.48M 0s
22500K .......... .......... .......... .......... .......... 73% 8.06M 0s
22550K .......... .......... .......... .......... .......... 73% 20.3M 0s
22600K .......... .......... .......... .......... .......... 73% 91.9M 0s
22650K .......... .......... .......... .......... .......... 73% 162M 0s
22700K .......... .......... .......... .......... .......... 73% 166M 0s
22750K .......... .......... .......... .......... .......... 74% 41.1M 0s
22800K .......... .......... .......... .......... .......... 74% 127M 0s
22850K .......... .......... .......... .......... .......... 74% 167M 0s
22900K .......... .......... .......... .......... .......... 74% 171M 0s
22950K .......... .......... .......... .......... .......... 74% 177M 0s
23000K .......... .......... .......... .......... .......... 74% 20.6M 0s
23050K .......... .......... .......... .......... .......... 75% 40.2M 0s
23100K .......... .......... .......... .......... .......... 75% 93.0M 0s
23150K .......... .......... .......... .......... .......... 75% 151M 0s
23200K .......... .......... .......... .......... .......... 75% 131M 0s
23250K .......... .......... .......... .......... .......... 75% 160M 0s
23300K .......... .......... .......... .......... .......... 75% 163M 0s
23350K .......... .......... .......... .......... .......... 76% 186M 0s
23400K .......... .......... .......... .......... .......... 76% 147M 0s
23450K .......... .......... .......... .......... .......... 76% 183M 0s
23500K .......... .......... .......... .......... .......... 76% 172M 0s
23550K .......... .......... .......... .......... .......... 76% 165M 0s
23600K .......... .......... .......... .......... .......... 76% 137M 0s
23650K .......... .......... .......... .......... .......... 77% 160M 0s
23700K .......... .......... .......... .......... .......... 77% 32.1M 0s
23750K .......... .......... .......... .......... .......... 77% 13.3M 0s
23800K .......... .......... .......... .......... .......... 77% 44.1M 0s
23850K .......... .......... .......... .......... .......... 77% 156M 0s
23900K .......... .......... .......... .......... .......... 77% 165M 0s
23950K .......... .......... .......... .......... .......... 78% 175M 0s
24000K .......... .......... .......... .......... .......... 78% 133M 0s
24050K .......... .......... .......... .......... .......... 78% 166M 0s
24100K .......... .......... .......... .......... .......... 78% 20.5M 0s
24150K .......... .......... .......... .......... .......... 78% 29.6M 0s
24200K .......... .......... .......... .......... .......... 78% 149M 0s
24250K .......... .......... .......... .......... .......... 79% 152M 0s
24300K .......... .......... .......... .......... .......... 79% 152M 0s
24350K .......... .......... .......... .......... .......... 79% 122M 0s
24400K .......... .......... .......... .......... .......... 79% 152M 0s
24450K .......... .......... .......... .......... .......... 79% 158M 0s
24500K .......... .......... .......... .......... .......... 79% 164M 0s
24550K .......... .......... .......... .......... .......... 79% 132M 0s
24600K .......... .......... .......... .......... .......... 80% 153M 0s
24650K .......... .......... .......... .......... .......... 80% 155M 0s
24700K .......... .......... .......... .......... .......... 80% 156M 0s
24750K .......... .......... .......... .......... .......... 80% 127M 0s
24800K .......... .......... .......... .......... .......... 80% 157M 0s
24850K .......... .......... .......... .......... .......... 80% 177M 0s
24900K .......... .......... .......... .......... .......... 81% 179M 0s
24950K .......... .......... .......... .......... .......... 81% 29.1M 0s
25000K .......... .......... .......... .......... .......... 81% 7.78M 0s
25050K .......... .......... .......... .......... .......... 81% 16.3M 0s
25100K .......... .......... .......... .......... .......... 81% 21.1M 0s
25150K .......... .......... .......... .......... .......... 81% 17.0M 0s
25200K .......... .......... .......... .......... .......... 82% 18.1M 0s
25250K .......... .......... .......... .......... .......... 82% 51.3M 0s
25300K .......... .......... .......... .......... .......... 82% 190M 0s
25350K .......... .......... .......... .......... .......... 82% 195M 0s
25400K .......... .......... .......... .......... .......... 82% 189M 0s
25450K .......... .......... .......... .......... .......... 82% 218M 0s
25500K .......... .......... .......... .......... .......... 83% 213M 0s
25550K .......... .......... .......... .......... .......... 83% 168M 0s
25600K .......... .......... .......... .......... .......... 83% 215M 0s
25650K .......... .......... .......... .......... .......... 83% 213M 0s
25700K .......... .......... .......... .......... .......... 83% 196M 0s
25750K .......... .......... .......... .......... .......... 83% 178M 0s
25800K .......... .......... .......... .......... .......... 84% 204M 0s
25850K .......... .......... .......... .......... .......... 84% 211M 0s
25900K .......... .......... .......... .......... .......... 84% 210M 0s
25950K .......... .......... .......... .......... .......... 84% 171M 0s
26000K .......... .......... .......... .......... .......... 84% 209M 0s
26050K .......... .......... .......... .......... .......... 84% 220M 0s
26100K .......... .......... .......... .......... .......... 85% 205M 0s
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26200K .......... .......... .......... .......... .......... 85% 5.87M 0s
26250K .......... .......... .......... .......... .......... 85% 196M 0s
26300K .......... .......... .......... .......... .......... 85% 219M 0s
26350K .......... .......... .......... .......... .......... 85% 180M 0s
26400K .......... .......... .......... .......... .......... 86% 208M 0s
26450K .......... .......... .......... .......... .......... 86% 216M 0s
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26550K .......... .......... .......... .......... .......... 86% 191M 0s
26600K .......... .......... .......... .......... .......... 86% 216M 0s
26650K .......... .......... .......... .......... .......... 86% 214M 0s
26700K .......... .......... .......... .......... .......... 86% 210M 0s
26750K .......... .......... .......... .......... .......... 87% 175M 0s
26800K .......... .......... .......... .......... .......... 87% 221M 0s
26850K .......... .......... .......... .......... .......... 87% 213M 0s
26900K .......... .......... .......... .......... .......... 87% 211M 0s
26950K .......... .......... .......... .......... .......... 87% 194M 0s
27000K .......... .......... .......... .......... .......... 87% 222M 0s
27050K .......... .......... .......... .......... .......... 88% 188M 0s
27100K .......... .......... .......... .......... .......... 88% 218M 0s
27150K .......... .......... .......... .......... .......... 88% 182M 0s
27200K .......... .......... .......... .......... .......... 88% 209M 0s
27250K .......... .......... .......... .......... .......... 88% 7.27M 0s
27300K .......... .......... .......... .......... .......... 88% 21.7M 0s
27350K .......... .......... .......... .......... .......... 89% 17.1M 0s
27400K .......... .......... .......... .......... .......... 89% 6.31M 0s
27450K .......... .......... .......... .......... .......... 89% 15.6M 0s
27500K .......... .......... .......... .......... .......... 89% 18.9M 0s
27550K .......... .......... .......... .......... .......... 89% 102M 0s
27600K .......... .......... .......... .......... .......... 89% 214M 0s
27650K .......... .......... .......... .......... .......... 90% 199M 0s
27700K .......... .......... .......... .......... .......... 90% 190M 0s
27750K .......... .......... .......... .......... .......... 90% 186M 0s
27800K .......... .......... .......... .......... .......... 90% 213M 0s
27850K .......... .......... .......... .......... .......... 90% 5.86M 0s
27900K .......... .......... .......... .......... .......... 90% 194M 0s
27950K .......... .......... .......... .......... .......... 91% 181M 0s
28000K .......... .......... .......... .......... .......... 91% 193M 0s
28050K .......... .......... .......... .......... .......... 91% 212M 0s
28100K .......... .......... .......... .......... .......... 91% 210M 0s
28150K .......... .......... .......... .......... .......... 91% 186M 0s
28200K .......... .......... .......... .......... .......... 91% 223M 0s
28250K .......... .......... .......... .......... .......... 92% 218M 0s
28300K .......... .......... .......... .......... .......... 92% 207M 0s
28350K .......... .......... .......... .......... .......... 92% 188M 0s
28400K .......... .......... .......... .......... .......... 92% 214M 0s
28450K .......... .......... .......... .......... .......... 92% 222M 0s
28500K .......... .......... .......... .......... .......... 92% 202M 0s
28550K .......... .......... .......... .......... .......... 92% 190M 0s
28600K .......... .......... .......... .......... .......... 93% 215M 0s
28650K .......... .......... .......... .......... .......... 93% 149M 0s
28700K .......... .......... .......... .......... .......... 93% 242M 0s
28750K .......... .......... .......... .......... .......... 93% 221M 0s
28800K .......... .......... .......... .......... .......... 93% 189M 0s
28850K .......... .......... .......... .......... .......... 93% 240M 0s
28900K .......... .......... .......... .......... .......... 94% 199M 0s
28950K .......... .......... .......... .......... .......... 94% 231M 0s
29000K .......... .......... .......... .......... .......... 94% 216M 0s
29050K .......... .......... .......... .......... .......... 94% 208M 0s
29100K .......... .......... .......... .......... .......... 94% 235M 0s
29150K .......... .......... .......... .......... .......... 94% 236M 0s
29200K .......... .......... .......... .......... .......... 95% 184M 0s
29250K .......... .......... .......... .......... .......... 95% 239M 0s
29300K .......... .......... .......... .......... .......... 95% 225M 0s
29350K .......... .......... .......... .......... .......... 95% 224M 0s
29400K .......... .......... .......... .......... .......... 95% 219M 0s
29450K .......... .......... .......... .......... .......... 95% 234M 0s
29500K .......... .......... .......... .......... .......... 96% 230M 0s
29550K .......... .......... .......... .......... .......... 96% 206M 0s
29600K .......... .......... .......... .......... .......... 96% 189M 0s
29650K .......... .......... .......... .......... .......... 96% 235M 0s
29700K .......... .......... .......... .......... .......... 96% 220M 0s
29750K .......... .......... .......... .......... .......... 96% 222M 0s
29800K .......... .......... .......... .......... .......... 97% 209M 0s
29850K .......... .......... .......... .......... .......... 97% 214M 0s
29900K .......... .......... .......... .......... .......... 97% 224M 0s
29950K .......... .......... .......... .......... .......... 97% 239M 0s
30000K .......... .......... .......... .......... .......... 97% 7.10M 0s
30050K .......... .......... .......... .......... .......... 97% 20.4M 0s
30100K .......... .......... .......... .......... .......... 98% 5.43M 0s
30150K .......... .......... .......... .......... .......... 98% 141M 0s
30200K .......... .......... .......... .......... .......... 98% 156M 0s
30250K .......... .......... .......... .......... .......... 98% 52.3M 0s
30300K .......... .......... .......... .......... .......... 98% 39.0M 0s
30350K .......... .......... .......... .......... .......... 98% 55.2M 0s
30400K .......... .......... .......... .......... .......... 99% 48.6M 0s
30450K .......... .......... .......... .......... .......... 99% 40.2M 0s
30500K .......... .......... .......... .......... .......... 99% 154M 0s
30550K .......... .......... .......... .......... .......... 99% 27.9M 0s
30600K .......... .......... .......... .......... .......... 99% 135M 0s
30650K .......... .......... .......... .......... .......... 99% 173M 0s
30700K .......... .......... .......... .......... .......... 99% 30.4M 0s
30750K ... 100% 59.1M=1.2s
2021-08-22 17:57:43 (25.7 MB/s) - ‘scarf_datasets/tenx_5K_pbmc_rnaseq/data.zarr.tar.gz’ saved [31491651/31491651]
INFO: Download finished! File saved here: scarf_datasets/tenx_5K_pbmc_rnaseq/data.zarr.tar.gz
time: 11.7 s (started: 2021-08-22 17:57:33 +00:00)
[4]:
ds = scarf.DataStore('scarf_datasets/tenx_5K_pbmc_rnaseq/data.zarr')
ds.plot_layout(layout_key='RNA_UMAP', color_by='RNA_cluster')
time: 1.76 s (started: 2021-08-22 17:57:45 +00:00)
3) Run TopACeDo downsampler¶
UMAP, clustering and marker identification together allow a good understanding of cellular diversity. However, one can still choose from a plethora of other analysis on the data. For example, identification of cell differentiation trajectories. One of the major challenges to run these analysis could be the size of the data. Scarf performs a topology conserving downsampling of the data based on the cell neighbourhood graph. This downsampling aims to maximize the heterogeneity while sampling cells from the data.
Here we run the TopACeDo downsampling algorithm that leverages Scarf’s KNN graph to perform a manifold preserving subsampling of cells. The subsampler can be invoked directly from Scarf’s DataStore object.
[5]:
ds.run_topacedo_sampler(cluster_key='RNA_cluster', max_sampling_rate=0.1)
Constructing graph from dendrogram: 100%|██████████| 3939/3939 [00:00<00:00, 21125.23it/s]
INFO: 384 cells (9.75%) sub-sampled. Subsample to Seed (165 cells) ratio: 2.327
INFO: Sketched cells saved under column 'RNA_sketched'
INFO: Cell neighbourhood densities saved under column: 'RNA_cell_density'
INFO: Mean SNN values saved under column: 'RNA_snn_value'
INFO: Seed cells saved under column: 'RNA_sketch_seeds'
time: 2.27 s (started: 2021-08-22 17:57:47 +00:00)
As a result of subsampling the subsampled cells are marked True under the cell metadata column RNA_sketched. We can visualize these cells using plot_layout
[6]:
ds.plot_layout(layout_key='RNA_UMAP', color_by='RNA_cluster', subselection_key='RNA_sketched')
time: 728 ms (started: 2021-08-22 17:57:49 +00:00)
It may also be interesting to visualize the cells that were marked as seed cells used when PCST was run. These cells are marked under the column RNA_sketch_seeds
[7]:
ds.plot_layout(layout_key='RNA_UMAP', color_by='RNA_cluster', subselection_key='RNA_sketch_seeds')
time: 703 ms (started: 2021-08-22 17:57:50 +00:00)
4) Intermediate parameters of downsampling¶
To identify the seed cells, the subsampling algorithm calculates cell densities based on neighbourhood degrees. Regions of higher cell density get a sampling penalty. The neighbourhood degree of individual cells are stored under the column RNA_cell_density
[8]:
ds.plot_layout(layout_key='RNA_UMAP', color_by='RNA_cell_density')
time: 1.19 s (started: 2021-08-22 17:57:51 +00:00)
The dowsampling algorithm also identififes regions of the graph where cells form tightly connected groups by calculating mean shared nearest neighbours of each cell’s nieghbours. The tightly connected regions get a sampling award. These values can be accessed from under the cell metadata column RNA_snn_value
[9]:
ds.plot_layout(layout_key='RNA_UMAP', color_by='RNA_snn_value')
time: 1.11 s (started: 2021-08-22 17:57:52 +00:00)
That is all for this vignette.