Skip to main content

Table 2 Running time of different functions in CytoTree with different cell numbers and marker numbers

From: CytoTree: an R/Bioconductor package for analysis and visualization of flow and mass cytometry data

Functions in CytoTree C 1*103
M 10
C 1*103
M 50
C 1*104
M 10
C 1*104
M 50
C 5*104
M: 10
C 5*104
M 50
C 1*105
M 10
C 1*105
M 50
C 5*105
M 10
C 5*105
M 50
createCYT 1s 1s 1s 1s 1s 1s 1s 2s 2s 2s
runCluster 1s 1s 1s 1s 2s 2s 2s 4s 5s 16s
processingCluster 1s 1s 1s 1s 2s 2s 2s 2s 2s 2s
runFastPCA* 1s 1s 1s 1s 2s 2s 2s 3s 9s 13s
runTSNE* 4s 4s 7s 1m35s 5m54s 13m22s 13m52s 36m30s 2h11m19s 10h57m17s
runDiffusionMap* 1s 2s 21s 36s 8m8s 18m42s 36m54s 1h35m15s 16h16m33s > 2 days
runUMAP* 5s 7s 1m32s 2m32s 9m17s 20m28s 21m35s 51m46s 2h17m28s 7h57m58s
buildTree 1s 1s 1s 1s 2s 2s 2s 2s 4s 8s
defRootCells 1s 1s 1s 1s 1s 1s 1s 1s 2s 2s
runPseudotime 1s 1s 9s 13s 3m17s 6m25s 5m46s 17m9s 12m41s 2h58m21s
defLeafCells 1s 1s 1s 1s 1s 1s 1s 1s 2s 2s
runWalk 1s 1s 7s 7s 2m1s 1m48s 2m1s 1m51s 2m18s 2m30s
Total time (all steps) 19s 22s 2m23s 5m10s 28m48s 1h56s 1h20m19s 3h22m46s 21h45s > 3 days
  1. C cell number, M marker number, 3h22m46s 3 hours 22 minutes and 46 seconds. Functions with * were optional steps, which are not the necessary steps in the CytoTree workflow. Calculation of total time contains all steps, including the optional steps
\