Reshape for 'make' functions
reshape_for_make_functions.RdThis internal function produces three primary datasets for the dashboard intended for the "make" functions.
Arguments
- data
The output of
pre_process()- cluster
The output of
gClusters()- annotation
The output of
gPathway()- id_colname
The columns that contain database IDs.
- id_type
The corresponding database names for the above columns.
Examples
data(test_data)
l <- reshape_for_make_functions(test_data_processed, test_cluster, test_annotations_processed, id_colname = c("GO_ID","KEGG_ID"),id_type = c("GO","KEGG"))
head(l[[1]])
#> ID cluster
#> 1 1 Group_2
#> 2 2 Group_5
#> 3 3 Group_2
#> 4 4 Group_4
#> 5 5 Group_4
#> 6 6 Group_2
#> GO_ID
#> 1
#> 2
#> 3 GO:0003674,GO:0003824,GO:0005575,GO:0006629,GO:0006644,GO:0006650,GO:0006655,GO:0006793,GO:0006796,GO:0008150,GO:0008152,GO:0008610,GO:0008654,GO:0008808,GO:0009058,GO:0009987,GO:0016020,GO:0016740,GO:0016772,GO:0016780,GO:0019637,GO:0030572,GO:0032048,GO:0032049,GO:0044237,GO:0044238,GO:0044249,GO:0044255,GO:0045017,GO:0046471,GO:0046474,GO:0046486,GO:0071704,GO:0090407,GO:1901576
#> 4 GO:0003674,GO:0003676,GO:0003723,GO:0003729,GO:0003824,GO:0004654,GO:0005488,GO:0005575,GO:0005622,GO:0005623,GO:0005737,GO:0006139,GO:0006401,GO:0006402,GO:0006725,GO:0006807,GO:0008150,GO:0008152,GO:0009056,GO:0009057,GO:0009892,GO:0009987,GO:0010468,GO:0010605,GO:0010629,GO:0016070,GO:0016071,GO:0016740,GO:0016772,GO:0016779,GO:0019222,GO:0019439,GO:0034641,GO:0034655,GO:0043170,GO:0044237,GO:0044238,GO:0044248,GO:0044260,GO:0044265,GO:0044270,GO:0044424,GO:0044464,GO:0046483,GO:0046700,GO:0048519,GO:0050789,GO:0060255,GO:0065007,GO:0071704,GO:0090304,GO:0097159,GO:1901360,GO:1901361,GO:1901363,GO:1901575
#> 5
#> 6
#> KEGG_ID Pathway taxonomic.scope
#> 1 K07124 Integumentary System hormonal proteins
#> 2 Skeletal System structural proteins
#> 3 K06131 Muscular System enzymes
#> 4 K00962 Nervous System contractile proteins
#> 5 K02083 Endocrine System contractile proteins
#> 6 Cardiovascular System structural proteins
head(l[[2]])
#> # A tibble: 6 × 6
#> ID type cluster day value taxonomic.scope
#> <int> <chr> <chr> <fct> <dbl> <chr>
#> 1 1 type_A Group_2 T1 -0.254 hormonal proteins
#> 2 1 type_A Group_2 T2 -0.676 hormonal proteins
#> 3 1 type_A Group_2 T3 -0.676 hormonal proteins
#> 4 1 type_A Group_2 T4 -0.254 hormonal proteins
#> 5 1 type_A Group_2 T5 -0.254 hormonal proteins
#> 6 1 type_A Group_2 T6 -0.676 hormonal proteins
head(l[[3]])
#> ID cluster
#> 1 1 Group_2
#> 2 2 Group_5
#> 3 3 Group_2
#> 4 4 Group_4
#> 5 5 Group_4
#> 6 6 Group_2
#> GO_ID
#> 1 <NA>
#> 2 <NA>
#> 3 <a href='https://www.ebi.ac.uk/QuickGO/term/GO:0003674' target='_blank'>GO:0003674</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0003824' target='_blank'>GO:0003824</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0005575' target='_blank'>GO:0005575</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0006629' target='_blank'>GO:0006629</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0006644' target='_blank'>GO:0006644</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0006650' target='_blank'>GO:0006650</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0006655' target='_blank'>GO:0006655</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0006793' target='_blank'>GO:0006793</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0006796' target='_blank'>GO:0006796</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0008150' target='_blank'>GO:0008150</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0008152' target='_blank'>GO:0008152</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0008610' target='_blank'>GO:0008610</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0008654' target='_blank'>GO:0008654</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0008808' target='_blank'>GO:0008808</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0009058' target='_blank'>GO:0009058</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0009987' target='_blank'>GO:0009987</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0016020' target='_blank'>GO:0016020</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0016740' target='_blank'>GO:0016740</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0016772' target='_blank'>GO:0016772</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0016780' target='_blank'>GO:0016780</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0019637' target='_blank'>GO:0019637</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0030572' target='_blank'>GO:0030572</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0032048' target='_blank'>GO:0032048</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0032049' target='_blank'>GO:0032049</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0044237' target='_blank'>GO:0044237</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0044238' target='_blank'>GO:0044238</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0044249' target='_blank'>GO:0044249</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0044255' target='_blank'>GO:0044255</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0045017' target='_blank'>GO:0045017</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0046471' target='_blank'>GO:0046471</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0046474' target='_blank'>GO:0046474</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0046486' target='_blank'>GO:0046486</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0071704' target='_blank'>GO:0071704</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0090407' target='_blank'>GO:0090407</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:1901576' target='_blank'>GO:1901576</a>
#> 4 <a href='https://www.ebi.ac.uk/QuickGO/term/GO:0003674' target='_blank'>GO:0003674</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0003676' target='_blank'>GO:0003676</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0003723' target='_blank'>GO:0003723</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0003729' target='_blank'>GO:0003729</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0003824' target='_blank'>GO:0003824</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0004654' target='_blank'>GO:0004654</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0005488' target='_blank'>GO:0005488</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0005575' target='_blank'>GO:0005575</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0005622' target='_blank'>GO:0005622</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0005623' target='_blank'>GO:0005623</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0005737' target='_blank'>GO:0005737</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0006139' target='_blank'>GO:0006139</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0006401' target='_blank'>GO:0006401</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0006402' target='_blank'>GO:0006402</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0006725' target='_blank'>GO:0006725</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0006807' target='_blank'>GO:0006807</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0008150' target='_blank'>GO:0008150</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0008152' target='_blank'>GO:0008152</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0009056' target='_blank'>GO:0009056</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0009057' target='_blank'>GO:0009057</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0009892' target='_blank'>GO:0009892</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0009987' target='_blank'>GO:0009987</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0010468' target='_blank'>GO:0010468</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0010605' target='_blank'>GO:0010605</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0010629' target='_blank'>GO:0010629</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0016070' target='_blank'>GO:0016070</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0016071' target='_blank'>GO:0016071</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0016740' target='_blank'>GO:0016740</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0016772' target='_blank'>GO:0016772</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0016779' target='_blank'>GO:0016779</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0019222' target='_blank'>GO:0019222</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0019439' target='_blank'>GO:0019439</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0034641' target='_blank'>GO:0034641</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0034655' target='_blank'>GO:0034655</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0043170' target='_blank'>GO:0043170</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0044237' target='_blank'>GO:0044237</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0044238' target='_blank'>GO:0044238</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0044248' target='_blank'>GO:0044248</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0044260' target='_blank'>GO:0044260</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0044265' target='_blank'>GO:0044265</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0044270' target='_blank'>GO:0044270</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0044424' target='_blank'>GO:0044424</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0044464' target='_blank'>GO:0044464</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0046483' target='_blank'>GO:0046483</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0046700' target='_blank'>GO:0046700</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0048519' target='_blank'>GO:0048519</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0050789' target='_blank'>GO:0050789</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0060255' target='_blank'>GO:0060255</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0065007' target='_blank'>GO:0065007</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0071704' target='_blank'>GO:0071704</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0090304' target='_blank'>GO:0090304</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:0097159' target='_blank'>GO:0097159</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:1901360' target='_blank'>GO:1901360</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:1901361' target='_blank'>GO:1901361</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:1901363' target='_blank'>GO:1901363</a><br/><a href='https://www.ebi.ac.uk/QuickGO/term/GO:1901575' target='_blank'>GO:1901575</a>
#> 5 <NA>
#> 6 <NA>
#> KEGG_ID
#> 1 <a href='https://www.kegg.jp/entry/K07124' target='_blank'>K07124</a>
#> 2 <NA>
#> 3 <a href='https://www.kegg.jp/entry/K06131' target='_blank'>K06131</a>
#> 4 <a href='https://www.kegg.jp/entry/K00962' target='_blank'>K00962</a>
#> 5 <a href='https://www.kegg.jp/entry/K02083' target='_blank'>K02083</a>
#> 6 <NA>
#> Pathway taxonomic.scope
#> 1 Integumentary System hormonal proteins
#> 2 Skeletal System structural proteins
#> 3 Muscular System enzymes
#> 4 Nervous System contractile proteins
#> 5 Endocrine System contractile proteins
#> 6 Cardiovascular System structural proteins