Get a single pathway
get_pathway(pathway_id)A BioCarta pathway ID. All valid BioCarta pathway IDs are in all_pathways().
To make it more convenient to use, the value can also be a MSigDB pathway ID in the BioCarta catalogue.
The format should look like: "BIOCARTA_RELA_PATHWAY".
A biocarta_pathway object. The object is a simple list and contains the following elements:
id: The pathway ID.
name: The pathway name.
bc: The nodes in the original BioCarta pathways are proteins and some of them do not have one-to-one
mapping to genes, such as protein families or complex. Here bc contains the primary IDs of proteins/single nodes in
the pathway. The mapping to genes can be obtained by genes_in_pathway().
shape: The shape of the corresponding protein/node in the pathway image.
coords: It is a list of integer vectors, which contains coordinates of the corresponding shapes, in the unit of pixels.
This information is retrieved from the HTML source code (in the <area> tag), so the the coordinates start from
the top left of the image. The format of the coordinate vectors is c(x1, y1, x2, y2, ...).
image_file: The file name of the pathway image.
The bc, shape and coords elements have the same length and in the same order.
The BioCarta pathways on MSigDB: https://www.gsea-msigdb.org/gsea/msigdb/human/genesets.jsp?collection=CP:BIOCARTA.
get_pathway("h_RELAPathway")
#> A BioCarta pathway:
#> ID: h_RELAPathway
#> Name: Acetylation and Deacetylation of RelA in The Nucleus
#> 35 nodes, 16 genes
get_pathway("BIOCARTA_RELA_PATHWAY")
#> A BioCarta pathway:
#> ID: h_RELAPathway
#> Name: Acetylation and Deacetylation of RelA in The Nucleus
#> 35 nodes, 16 genes