pathfindR (version 1.3.0)

visualize_pws: Create Pathway Diagrams

Description

Create Pathway Diagrams

Usage

visualize_pws(result_df, input_processed = NULL, gene_sets = "KEGG",
  pin_name_path = "Biogrid")

Arguments

result_df

Data frame of enrichment results. Must-have columns for KEGG human pathway diagrams are: "ID" and "Pathway". Must-have columns for the rest are: "Pathway", "Up_regulated" and "Down_regulated"

input_processed

input data processed via `input_processing`, not necessary for visualizations other than KEGG human pathway diagrams.

gene_sets

the gene sets used for enrichment analysis. Possible gene sets are KEGG, Reactome, BioCarta, GO-All, GO-BP, GO-CC, GO-MF or Custom (Default = "KEGG").

pin_name_path

Name of the chosen PIN or path/to/PIN.sif. If PIN name, must be one of c("Biogrid", "GeneMania", "IntAct", "KEGG"). If path/to/PIN.sif, the file must comply with the PIN specifications. Defaults to Biogrid.

Value

Depending of `gene_sets`, creates visualization of interactions of genes involved in the list of pathways in `result_df` and saves them in the folder "pathway_visualizations" under the current working directory.

Details

For `gene_sets == "KEGG"`, KEGG human pathway diagrams are created, affected nodes colored by up/down regulation status. For the rest of `gene_sets`, interactions of affected genes are determined (via a shortest-path algorithm) and are visualized (colored by change status) using igraph.

See Also

See visualize_hsa_KEGG for the visualization function of human KEGG diagrams. See visualize_pw_interactions for the visualization function that generates diagrams showing the interactions of input genes in the PIN. See run_pathfindR for the wrapper function of the pathfindR workflow. pathview for KEGG pathway-based data integration and visualization.

Examples

# NOT RUN {
visualize_pws(result_df, input_processed)
visualize_pws(result_df, gene_sets = "GO-BP", pin_name_path = "IntAct")
# }