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

BMC Bioinformatics

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

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

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

ISSN: 1471-2105