## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 8, fig.height = 4, fig.align = "center"
)
suppressPackageStartupMessages(library(pathfindR))

## ----compare2res--------------------------------------------------------------
combined_df <- combine_pathfindR_results(result_A = RA_output, 
                                         result_B = RA_comparison_output, 
                                         plot_common = FALSE)

## ----compare_graph1-----------------------------------------------------------
combined_results_graph(combined_df)

## ----compare_graph2, fig.width=8, fig.height=4--------------------------------
combined_results_graph(combined_df, 
                       selected_terms = c("hsa04144", "hsa04141", "hsa04140"))

## ----compare_graph3, eval=FALSE-----------------------------------------------
#  combined_results_graph(combined_df,
#                         use_description = TRUE,
#                         selected_terms = combined_df$Term_Description[1:4])

## ----compare_graph4, eval=FALSE-----------------------------------------------
#  combined_results_graph(combined_df,
#                         selected_terms = c("hsa04144", "hsa04141", "hsa04140"),
#                         node_size = "p_val")

