pathmap: Annotate Involved Genes In Pathways and Visualize Pathways
Description
Annotate Involved Genes In Pathways and Visualize Pathways
Usage
pathmap(pw_table, gene_data)
Arguments
pw_table
Data frame of enrichment results. Must-have columns are: "ID" and
"Pathway".
gene_data
Single column data frame containing change values (e.g.
log(fold change) values) for significant genes. Row names are gene symbols.
Value
The function returns the input data frame with genes involved in each pathway.
Added columns are: "Up_regulated" and "Down_regulated", the up- and down-regulated genes,
respectively. The function also creates visualizations of the pathways with
the package pathview and saves them in the folder "pathway_maps"
under the current working directory.
See Also
pathview for pathway-based data integration
and visualization. See run_pathfindR for the wrapper function
of the pathfindR workflow