Which genes should appear at the top of the oncoplot? This function takes pathway and gene ranks and returns a list of genes sorted first by pathway then by gene rank. Gene & pathway rankings can be calculated upstream. By default will use their order in gene_pathway_map.
Usage
rank_genes_based_on_pathways(
gene_pathway_map,
generanks = unique(as.character(gene_pathway_map[[1]])),
pathwayranks = unique(as.character(gene_pathway_map[[2]]))
)Arguments
- gene_pathway_map
dataframe where column 1 = gene names and column 2 = pathway names
- generanks
gene names in the order they should be ranked, where earlier in vector = further up in oncoplot. (character)
- pathwayranks
pathway names in the order they should be ranked, where earlier in vector = further up in oncoplot (character)