Partition the DAG
partition_by_level(dag, level = 1, from = NULL, term_pos = NULL)
partition_by_size(dag, size = round(dag_n_terms(dag)/5))An ontology_DAG object.
Depth in the DAG to cut. The DAG is cut below terms (or cut the links to their child terms) with depth == level.
A list of terms to cut. If it is set, level is ignored.
Internally used.
Number of terms in a cluster. The splitting stops on a term if all its child-trees are smaller than size.
A character vector of top terms in each partition.
Let's call the terms below the from term as "top terms" because they will be on top of the sub-DAGs after the partitioning.
It is possible that a term in the middle of the DAG can be traced back to more than one top terms.
To partition all terms exclusively, a term partitioned to the sub-DAG from the top term with the largest distance to the term.
If a term has the same largest distances to several top terms, a random top term is selected.
In partition_by_size(), the DAG is first reduced to a tree where a child term only has one parent.
The partition is done recursively by cutting into its child-trees.
The splitting stops when all the child-trees have size less than size.
NA is assigned to the from terms, their ancestor terms, and terms having infinite directed distance to from terms.
# \donttest{
dag = create_ontology_DAG_from_GO_db()
#> relations: is_a, part_of
pa = partition_by_level(dag)
#>
#> going through 1000 / 27942 nodes ...
#>
#> going through 2000 / 27942 nodes ...
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#> going through 3000 / 27942 nodes ...
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#> going through 4000 / 27942 nodes ...
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#> going through 5000 / 27942 nodes ...
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#> going through 6000 / 27942 nodes ...
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#> going through 7000 / 27942 nodes ...
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#> going through 8000 / 27942 nodes ...
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#> going through 9000 / 27942 nodes ...
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#> going through 10000 / 27942 nodes ...
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#> going through 11000 / 27942 nodes ...
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#> going through 12000 / 27942 nodes ...
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#> going through 13000 / 27942 nodes ...
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#> going through 14000 / 27942 nodes ...
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#> going through 15000 / 27942 nodes ...
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#> going through 16000 / 27942 nodes ...
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#> going through 17000 / 27942 nodes ...
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#> going through 18000 / 27942 nodes ...
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#> going through 19000 / 27942 nodes ...
#>
#> going through 20000 / 27942 nodes ...
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#> going through 21000 / 27942 nodes ...
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#> going through 22000 / 27942 nodes ...
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#> going through 23000 / 27942 nodes ...
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#> going through 24000 / 27942 nodes ...
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#> going through 25000 / 27942 nodes ...
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#> going through 26000 / 27942 nodes ...
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#> going through 27000 / 27942 nodes ...
#>
#> going through 27942 / 27942 nodes ... Done.
#>
#> going through 1000 / 27942 nodes ...
#>
#> going through 2000 / 27942 nodes ...
#>
#> going through 3000 / 27942 nodes ...
#>
#> going through 4000 / 27942 nodes ...
#>
#> going through 5000 / 27942 nodes ...
#>
#> going through 6000 / 27942 nodes ...
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#> going through 7000 / 27942 nodes ...
#>
#> going through 8000 / 27942 nodes ...
#>
#> going through 9000 / 27942 nodes ...
#>
#> going through 10000 / 27942 nodes ...
#>
#> going through 11000 / 27942 nodes ...
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#> going through 12000 / 27942 nodes ...
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#> going through 13000 / 27942 nodes ...
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#> going through 14000 / 27942 nodes ...
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#> going through 15000 / 27942 nodes ...
#>
#> going through 16000 / 27942 nodes ...
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#> going through 17000 / 27942 nodes ...
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#> going through 18000 / 27942 nodes ...
#>
#> going through 19000 / 27942 nodes ...
#>
#> going through 20000 / 27942 nodes ...
#>
#> going through 21000 / 27942 nodes ...
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#> going through 22000 / 27942 nodes ...
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#> going through 23000 / 27942 nodes ...
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#> going through 24000 / 27942 nodes ...
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#> going through 25000 / 27942 nodes ...
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#> going through 26000 / 27942 nodes ...
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#> going through 27000 / 27942 nodes ...
#>
#> going through 27942 / 27942 nodes ... Done.
table(pa)
#> pa
#> GO:0000003 GO:0002376 GO:0008152 GO:0009987 GO:0016032 GO:0023052 GO:0032501
#> 238 104 5904 2198 89 1 581
#> GO:0032502 GO:0040007 GO:0040011 GO:0042592 GO:0043473 GO:0044419 GO:0044848
#> 3752 19 6 137 5 377 61
#> GO:0048511 GO:0050896 GO:0051179 GO:0051703 GO:0065007
#> 3 1938 1760 1 10767
pa = partition_by_size(dag, size = 1000)
#>
#> going through 1000 / 27942 nodes ...
#>
#> going through 2000 / 27942 nodes ...
#>
#> going through 3000 / 27942 nodes ...
#>
#> going through 4000 / 27942 nodes ...
#>
#> going through 5000 / 27942 nodes ...
#>
#> going through 6000 / 27942 nodes ...
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#> going through 7000 / 27942 nodes ...
#>
#> going through 8000 / 27942 nodes ...
#>
#> going through 9000 / 27942 nodes ...
#>
#> going through 10000 / 27942 nodes ...
#>
#> going through 11000 / 27942 nodes ...
#>
#> going through 12000 / 27942 nodes ...
#>
#> going through 13000 / 27942 nodes ...
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#> going through 14000 / 27942 nodes ...
#>
#> going through 15000 / 27942 nodes ...
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#> going through 16000 / 27942 nodes ...
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#> going through 17000 / 27942 nodes ...
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#> going through 18000 / 27942 nodes ...
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#> going through 19000 / 27942 nodes ...
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#> going through 20000 / 27942 nodes ...
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#> going through 21000 / 27942 nodes ...
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#> going through 22000 / 27942 nodes ...
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#> going through 23000 / 27942 nodes ...
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#> going through 24000 / 27942 nodes ...
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#> going through 25000 / 27942 nodes ...
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#> going through 26000 / 27942 nodes ...
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#> going through 27000 / 27942 nodes ...
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#> going through 27942 / 27942 nodes ... Done.
table(pa)
#> pa
#> GO:0000003 GO:0001748 GO:0001775 GO:0001887 GO:0001906 GO:0002376 GO:0002682
#> 238 1 82 1 5 104 297
#> GO:0003360 GO:0006081 GO:0006082 GO:0006091 GO:0006116 GO:0006139 GO:0006276
#> 1 20 874 68 1 1462 4
#> GO:0006457 GO:0006730 GO:0006735 GO:0006749 GO:0006790 GO:0006793 GO:0006807
#> 10 2 1 3 41 166 389
#> GO:0006810 GO:0006950 GO:0007017 GO:0007049 GO:0007154 GO:0007155 GO:0007163
#> 1298 174 12 82 112 46 15
#> GO:0007389 GO:0007552 GO:0007562 GO:0007568 GO:0008037 GO:0008218 GO:0008219
#> 160 1 2 1 7 1 77
#> GO:0008283 GO:0009056 GO:0009058 GO:0009292 GO:0009605 GO:0009607 GO:0009628
#> 50 46 55 5 458 40 123
#> GO:0009653 GO:0009698 GO:0009719 GO:0009790 GO:0009791 GO:0009812 GO:0009838
#> 238 63 27 216 104 17 4
#> GO:0009888 GO:0009889 GO:0009892 GO:0009893 GO:0009894 GO:0010098 GO:0010118
#> 190 230 63 64 54 1 3
#> GO:0010191 GO:0010259 GO:0010712 GO:0014823 GO:0014854 GO:0015977 GO:0015979
#> 8 1 1 4 4 2 1
#> GO:0016032 GO:0016043 GO:0016049 GO:0016999 GO:0018884 GO:0018893 GO:0018894
#> 89 1173 4 1 1 1 1
#> GO:0018930 GO:0018933 GO:0018942 GO:0018955 GO:0018958 GO:0019438 GO:0019439
#> 1 1 10 1 85 1 12
#> GO:0019536 GO:0019748 GO:0019835 GO:0021700 GO:0022406 GO:0022611 GO:0023051
#> 1 26 1 2 6 14 3
#> GO:0023052 GO:0030029 GO:0031099 GO:0031128 GO:0031137 GO:0031323 GO:0031413
#> 1 14 24 4 9 1181 1
#> GO:0031503 GO:0032196 GO:0032259 GO:0032501 GO:0032879 GO:0032963 GO:0033013
#> 16 3 1 581 1211 1 51
#> GO:0033036 GO:0033059 GO:0034337 GO:0035188 GO:0035212 GO:0035295 GO:0036166
#> 380 1 2 2 1 86 3
#> GO:0040007 GO:0040008 GO:0040011 GO:0040012 GO:0042180 GO:0042221 GO:0042335
#> 19 81 6 221 31 1104 11
#> GO:0042430 GO:0042440 GO:0042537 GO:0042558 GO:0042592 GO:0042620 GO:0042752
#> 9 22 61 6 137 2 4
#> GO:0043094 GO:0043170 GO:0043335 GO:0043455 GO:0043473 GO:0043696 GO:0043903
#> 3 1093 1 1 5 6 20
#> GO:0043934 GO:0044085 GO:0044145 GO:0044238 GO:0044281 GO:0044419 GO:0044848
#> 2 19 6 756 64 377 61
#> GO:0045103 GO:0045730 GO:0046483 GO:0046950 GO:0048229 GO:0048511 GO:0048513
#> 1 1 22 1 27 3 117
#> GO:0048518 GO:0048519 GO:0048583 GO:0048589 GO:0048647 GO:0048731 GO:0048736
#> 133 149 533 4 6 2406 54
#> GO:0048857 GO:0048869 GO:0048870 GO:0050792 GO:0050793 GO:0050794 GO:0051171
#> 1 268 95 20 1161 3000 394
#> GO:0051235 GO:0051239 GO:0051301 GO:0051606 GO:0051640 GO:0051641 GO:0051649
#> 16 435 17 1 46 10 1
#> GO:0051656 GO:0051674 GO:0051703 GO:0051716 GO:0051775 GO:0052803 GO:0060021
#> 1 1 1 41 2 5 6
#> GO:0060255 GO:0060263 GO:0060322 GO:0060352 GO:0061027 GO:0061061 GO:0061842
#> 515 1 3 1 1 3 3
#> GO:0061919 GO:0062012 GO:0062097 GO:0065008 GO:0065009 GO:0070085 GO:0070121
#> 1 9 1 158 400 4 1
#> GO:0070988 GO:0071554 GO:0071696 GO:0071728 GO:0072059 GO:0072521 GO:0072592
#> 2 3 4 1 2 4 1
#> GO:0072593 GO:0080090 GO:0090345 GO:0090399 GO:0090618 GO:0097006 GO:0097354
#> 7 362 2 1 1 9 1
#> GO:0097737 GO:0098727 GO:0098743 GO:0099120 GO:0106336 GO:0110051 GO:0120161
#> 1 7 15 16 1 1 1
#> GO:0120246 GO:0120252 GO:0120254 GO:0120305 GO:0120312 GO:0140253 GO:0160062
#> 9 39 5 20 1 1 1
#> GO:1900558 GO:1900594 GO:1900597 GO:1900619 GO:1900819 GO:1900908 GO:1901125
#> 3 1 1 4 1 2 3
#> GO:1901135 GO:1901275 GO:1901286 GO:1901360 GO:1901440 GO:1901615 GO:1901764
#> 134 1 1 3 10 163 1
#> GO:1901902 GO:1902421 GO:1903664 GO:1903700 GO:1903701 GO:1903866 GO:1903867
#> 1 1 1 1 1 1 5
#> GO:1904817 GO:1904888 GO:1905328 GO:1990045 GO:1990845 GO:2000241 GO:2001290
#> 4 1 1 1 2 14 1
# }
1
#> [1] 1