GetTransitionsAsEdges
GetTransitionsAsEdges.RdGiven a TrackSOM clustering and tracking, descramble the meta-cluster ID. Handy to work out the meta-cluster transitions.
Examples
library(data.table)
data_files <- sapply(c(0:4), function(i) {
system.file("extdata", paste0("synthetic_d", i, ".fcs"), package="TrackSOM")
})
use_cols <- c("x", "y", "z")
tracksom_result <- TrackSOM(inputFiles = data_files,
colsToUse = use_cols,
nClus = 10,
dataFileType = ".fcs"
)
#> Reading file /home/runner/work/_temp/Library/TrackSOM/extdata/synthetic_d0.fcs
#> Reading file /home/runner/work/_temp/Library/TrackSOM/extdata/synthetic_d1.fcs
#> Reading file /home/runner/work/_temp/Library/TrackSOM/extdata/synthetic_d2.fcs
#> Reading file /home/runner/work/_temp/Library/TrackSOM/extdata/synthetic_d3.fcs
#> Reading file /home/runner/work/_temp/Library/TrackSOM/extdata/synthetic_d4.fcs
#> Building SOM
#> Mapping data to SOM
#> Building MST
#> Extracting SOM nodes for each time point
#> Running meta clustering
#> Meta clustering time point 1 with 83 SOM nodes
#> Meta clustering time point 2 with 90 SOM nodes
#> Meta clustering time point 3 with 93 SOM nodes
#> Meta clustering time point 4 with 95 SOM nodes
#> Meta clustering time point 5 with 93 SOM nodes
data <- lapply(c(0:4), function(i) {
fread(system.file("extdata", paste0("synthetic_d", i, ".csv"), package="TrackSOM"))
})
data <- rbindlist(data)
tracksom_res <- ConcatenateClusteringDetails(
dat = data,
tracksom.result = tracksom_result,
timepoint.col = 'timepoint',
timepoints = c("Mock", "SYN-1", "SYN-2", "SYN-3", "SYN-4")
)
GetTransitionsAsEdges(dat = tracksom_res,
timepoint_col = 'timepoint',
timepoints = c("Mock", "SYN-1", "SYN-2", "SYN-3", "SYN-4"),
cluster_col = "TrackSOM_metacluster_lineage_tracking")
#> from
#> 1 1_C
#> 2 1_J
#> 3 1_G
#> 4 1_B
#> 5 1_A
#> 6 1_G
#> 7 1_B
#> 8 1_E
#> 9 1_D
#> 10 1_E
#> 11 1_H
#> 12 1_F
#> 13 1_C
#> 14 1_E
#> 15 1_H
#> 16 1_G
#> 17 2_(D,E)
#> 18 2_E|1
#> 19 2_E|1
#> 20 2_(G|2,H|1)
#> 21 2_(A,B|1,G|1)
#> 22 2_C|1
#> 23 2_C|1
#> 24 2_(A,B|1,G|1)
#> 25 2_(B,G)
#> 26 2_(F,H)
#> 27 2_J
#> 28 2_J
#> 29 3_(D,E)
#> 30 3_E|1
#> 31 3_E|1
#> 32 3_K
#> 33 3_L
#> 34 3_J|1
#> 35 3_J|1
#> 36 3_((A,B|1,G|1)|1,(B,G))
#> 37 3_((A,B|1,G|1),C|1)
#> 38 3_((F,H),J)
#> 39 3_M
#> 40 3_((A,B|1,G|1),C|1)
#> 41 3_(G|2,H|1)
#> 42 3_((A,B|1,G|1),C|1)
#> 43 3_(G|2,H|1)
#> 44 4_(D,E)
#> 45 4_E|1
#> 46 4_E|1
#> 47 4_(((A,B|1,G|1),C|1),((A,B|1,G|1)|1,(B,G)))
#> 48 4_(((F,H),J),M)
#> 49 4_(((A,B|1,G|1),C|1)|1,(G|2,H|1))
#> 50 4_((A,B|1,G|1),C|1)|2
#> 51 4_(G|2,H|1)|1
#> 52 4_(((F,H),J),M)
#> 53 4_J|1
#> 54 4_J|1
#> 55 4_(((A,B|1,G|1),C|1)|1,(G|2,H|1))
#> to
#> 1 2_C
#> 2 2_J
#> 3 2_(A,B|1,G|1)
#> 4 2_(A,B|1,G|1)
#> 5 2_(A,B|1,G|1)
#> 6 2_(B,G)
#> 7 2_(B,G)
#> 8 2_(D,E)
#> 9 2_(D,E)
#> 10 2_E|1
#> 11 2_(F,H)
#> 12 2_(F,H)
#> 13 2_C|1
#> 14 2_E|2
#> 15 2_(G|2,H|1)
#> 16 2_(G|2,H|1)
#> 17 3_(D,E)
#> 18 3_E|1
#> 19 3_E|1
#> 20 3_(G|2,H|1)
#> 21 3_((A,B|1,G|1),C|1)
#> 22 3_((A,B|1,G|1),C|1)
#> 23 3_((A,B|1,G|1),C|1)
#> 24 3_((A,B|1,G|1)|1,(B,G))
#> 25 3_((A,B|1,G|1)|1,(B,G))
#> 26 3_((F,H),J)
#> 27 3_((F,H),J)
#> 28 3_J|1
#> 29 4_(D,E)
#> 30 4_E|1
#> 31 4_E|1
#> 32 4_K
#> 33 4_L
#> 34 4_J|1
#> 35 4_J|1
#> 36 4_(((A,B|1,G|1),C|1),((A,B|1,G|1)|1,(B,G)))
#> 37 4_(((A,B|1,G|1),C|1),((A,B|1,G|1)|1,(B,G)))
#> 38 4_(((F,H),J),M)
#> 39 4_(((F,H),J),M)
#> 40 4_(((A,B|1,G|1),C|1)|1,(G|2,H|1))
#> 41 4_(((A,B|1,G|1),C|1)|1,(G|2,H|1))
#> 42 4_((A,B|1,G|1),C|1)|2
#> 43 4_(G|2,H|1)|1
#> 44 5_(D,E)
#> 45 5_E|1
#> 46 5_E|1
#> 47 5_(((A,B|1,G|1),C|1),((A,B|1,G|1)|1,(B,G)))
#> 48 5_(((F,H),J),M)
#> 49 5_(((A,B|1,G|1),C|1)|1,(G|2,H|1))
#> 50 5_((A,B|1,G|1),C|1)|2
#> 51 5_(G|2,H|1)|1
#> 52 5_((((F,H),J),M)|1,J|1)
#> 53 5_((((F,H),J),M)|1,J|1)
#> 54 5_((((F,H),J),M)|1,J|1)
#> 55 5_(((A,B|1,G|1),C|1)|1,(G|2,H|1))|1