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

## ----setup--------------------------------------------------------------------
suppressPackageStartupMessages(library(pathfindR))

## ----enr_chart, eval=FALSE----------------------------------------------------
# enrichment_chart(example_pathfindR_output)

## ----enr_chart2, eval=FALSE---------------------------------------------------
# ## change top_terms
# enrichment_chart(example_pathfindR_output, top_terms = 3)
# 
# ## set null for displaying all terms
# enrichment_chart(example_pathfindR_output, top_terms = NULL)

## ----enr_chart3, fig.height=8, fig.width=8------------------------------------
enrichment_chart(example_pathfindR_output_clustered, plot_by_cluster = TRUE)

## ----KEGG_vis, eval=FALSE-----------------------------------------------------
# input_processed <- input_processing(example_pathfindR_input)
# gg_list <- visualize_terms(
#   result_df = example_pathfindR_output,
#   input_processed = input_processed,
#   is_KEGG_result = TRUE
# ) # this function returns a list of ggraph objects (named by Term ID)
# 
# # save one of the plots as PDF image
# ggplot2::ggsave(
#   "hsa04911_diagram.pdf",
#   gg_list$hsa04911,
#   width = 5,
#   height = 5
# )

## ----nonKEGG_viss, eval=FALSE-------------------------------------------------
# input_processed <- input_processing(example_pathfindR_input)
# gg_list <- visualize_terms(
#   result_df = example_pathfindR_output,
#   input_processed = input_processed,
#   is_KEGG_result = FALSE,
#   pin_name_path = "Biogrid"
# ) # this function returns a list of ggraph objects (named by Term ID)
# 
# # save one of the plots as PDF image
# ggplot2::ggsave(
#   "diabetic_cardiomyopathy_interactions.pdf",
#   gg_list$hsa04911,
#   width = 10,
#   height = 6
# )

## ----hmap---------------------------------------------------------------------
term_gene_heatmap(example_pathfindR_output)

## ----hmap2, eval=FALSE--------------------------------------------------------
# term_gene_heatmap(example_pathfindR_output, num_terms = 3)
# 
# ## set null for displaying all terms
# term_gene_heatmap(example_pathfindR_output, num_terms = NULL)

## ----hmap3, eval=FALSE--------------------------------------------------------
# term_gene_heatmap(example_pathfindR_output, use_description = TRUE)

## ----hmap4, eval=FALSE--------------------------------------------------------
# term_gene_heatmap(result_df = example_pathfindR_output, genes_df = example_pathfindR_input)

## ----term_gene1---------------------------------------------------------------
g <- create_term_gene_graph(example_pathfindR_output)
create_term_gene_plot(g)

## ----term_gene2, eval=FALSE---------------------------------------------------
# g <- create_term_gene_graph(example_pathfindR_output, num_terms = NULL)
# create_term_gene_plot(g)

## ----term_gene3---------------------------------------------------------------
g <- create_term_gene_graph(example_pathfindR_output, num_terms = 3, use_description = TRUE)
create_term_gene_plot(g)

## ----term_gene4, eval=FALSE---------------------------------------------------
# create_term_gene_graph(example_pathfindR_output, num_terms = 3, term_size = "p_val")

## ----term_gene5---------------------------------------------------------------
g <- create_term_gene_graph(
  result_df = pathfindR.data::example_pathfindR_output,
  genes_df = pathfindR.data::example_pathfindR_input,
  term_fill = "Fold_Enrichment",
  num_terms = 3,
  use_edge_weights = TRUE
)
create_term_gene_plot(g)

## ----upset1-------------------------------------------------------------------
UpSet_plot(example_pathfindR_output)

## ----upset2, eval=FALSE-------------------------------------------------------
# UpSet_plot(example_pathfindR_output, genes_df = example_pathfindR_input)

## ----upset3, eval=FALSE-------------------------------------------------------
# UpSet_plot(example_pathfindR_output, num_terms = 5)

## ----upset4, eval=FALSE-------------------------------------------------------
# UpSet_plot(example_pathfindR_output, use_description = TRUE)

## ----upset5, eval=FALSE-------------------------------------------------------
# UpSet_plot(example_pathfindR_output, method = "barplot")

## ----upset6, eval=FALSE-------------------------------------------------------
# UpSet_plot(example_pathfindR_output, example_pathfindR_input, method = "boxplot")