Generate processed annotation
gAnnotation.RdgAnnotation() provides the standard input format for the dashboard, allowing users to select two columns as the primary factors they wish to visualize and describe in the data.
Arguments
- data
A data.frame containing annotations that should be used for describing the features we measured at each time point. It is also required to include
IDand at least two categorical variables.- first_order
A string. The name of one column of categorical variable in
data.- second_order
A string. The name of another column of categorical variable in
data.
Details
Guidelines for Selecting Annotations:
The first-order annotation is recommended to be functional, such as a pathway or functional system. This parameter will primarily serve the purpose of filtering out one network at a time when displaying the dashboard.
The second-order annotation is utilized to illustrate the composition of a first-order annotation using a bar plot. Therefore, it is better to set it as taxon, class label, etc.
Examples
data(test_data)
test_annotations_processed <- gAnnotation(test_annotations,system,class)
head(test_annotations_processed)
#> ID
#> 1 1
#> 2 2
#> 3 3
#> 4 4
#> 5 5
#> 6 6
#> 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