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GregorySchwartz / too-many-cells

Cluster single cells and analyze cell clade relationships with colorful visualizations.
https://gregoryschwartz.github.io/too-many-cells/
GNU General Public License v3.0
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Running a million cells failed in the docker #34

Closed minghlijiyi closed 4 years ago

minghlijiyi commented 4 years ago

Hi Gregory, I installed the package in the docker. I gave 15g RAM to the docker, it is the maximum RAM. It runs well for 500,000 cells, However, it runs failed for a million cells. Could you give me some help? I used the below codes. Thank you. docker run -it --rm -v "/home/username:/home/username" \ -m 15g \ gregoryschwartz/too-many-cells:2.0.0.0 make-tree \ --matrix-path /home/username/path/to/input \ --labels-file /home/username/path/to/labels.csv \ --draw-collection "PieRing" \ --output /home/username/path/to/out \

clusters.csv

GregorySchwartz commented 4 years ago

too-many-cells will try to use all features for the most accurate result. However, with many cells this will take even more time and space. I recommend using dimensionality reduction to reduce the feature space upstream of too-many-cells, or try using the built in one (--lsa) to see if it can handle it first.

minghlijiyi commented 4 years ago

It works, thank you so much!