--- a/pathview.r	Mon May 09 20:12:57 2022 +0000
+++ b/pathview.r	Mon Mar 23 13:46:44 2026 +0000
@@ -1,6 +1,6 @@
 error_foo <- function() {
-  cat(geterrmessage(), file = stderr());
-  q("no", 1, F)
+    cat(geterrmessage(), file = stderr())
+    q("no", 1, F)
 }
 options(show.error.messages = F, error = error_foo)
 
@@ -15,24 +15,24 @@
 sessionInfo()
 
 option_list <- list(
-  make_option(c("--pathway_id"), type = "character", default = NULL, help = "Path to tabular file with gene data"),
-  make_option(c("--pathway_id_fp"), type = "character", default = NULL, help = "Path to tabular file with pathway ids"),
-  make_option(c("--pathway_id_header"), type = "logical", default = FALSE, help = "Header for tabular file with pathway ids"),
-  make_option(c("--species"), type = "character", default = "hsa", help = "KEGG code, scientific name or the common name of the species"),
-  make_option(c("--gene_data"), type = "character", default = NULL, help = "Path to tabular file with gene data"),
-  make_option(c("--gd_header"), type = "logical", default = FALSE, help = "Header for the gene data file"),
-  make_option(c("--gene_idtype"), type = "character", default = "entrez", help = "ID type used for the gene data"),
-  make_option(c("--cpd_data"), type = "character", default = NULL, help = "Path to tabular file with compound data"),
-  make_option(c("--cpd_header"), type = "logical", default = FALSE, help = "Header for the compound data file"),
-  make_option(c("--cpd_idtype"), type = "character", default = "kegg", help = "ID type used for the compound data"),
-  make_option(c("--multi_state"), type = "logical", default = TRUE, help = "Are the gene and compound data paired?"),
-  make_option(c("--match_data"), type = "logical", default = TRUE, help = "Are the gene and compound data paired?"),
-  make_option(c("--kegg_native"), type = "logical", default = TRUE, help = "Render pathway graph as native KEGG grap? Alternative is the Graphviz layout"),
-  make_option(c("--same_layer"), type = "logical", default = TRUE, help = "Plot on same layer?"),
-  make_option(c("--map_null"), type = "logical", default = TRUE, help = "Map the NULL gene or compound data to pathway?"),
-  make_option(c("--split_group"), type = "logical", default = FALSE, help = "Split node groups into individual nodes?"),
-  make_option(c("--expand_node"), type = "logical", default = FALSE, help = "Expand multiple-gene nodes into single-gene nodes?"),
-  make_option(c("--sign_pos"), type = "character", default = "bottomright", help = "Position of pathview signature")
+    make_option(c("--pathway_id"), type = "character", default = NULL, help = "Path to tabular file with gene data"),
+    make_option(c("--pathway_id_fp"), type = "character", default = NULL, help = "Path to tabular file with pathway ids"),
+    make_option(c("--pathway_id_header"), type = "logical", default = FALSE, help = "Header for tabular file with pathway ids"),
+    make_option(c("--species"), type = "character", default = "hsa", help = "KEGG code, scientific name or the common name of the species"),
+    make_option(c("--gene_data"), type = "character", default = NULL, help = "Path to tabular file with gene data"),
+    make_option(c("--gd_header"), type = "logical", default = FALSE, help = "Header for the gene data file"),
+    make_option(c("--gene_idtype"), type = "character", default = "entrez", help = "ID type used for the gene data"),
+    make_option(c("--cpd_data"), type = "character", default = NULL, help = "Path to tabular file with compound data"),
+    make_option(c("--cpd_header"), type = "logical", default = FALSE, help = "Header for the compound data file"),
+    make_option(c("--cpd_idtype"), type = "character", default = "kegg", help = "ID type used for the compound data"),
+    make_option(c("--multi_state"), type = "logical", default = TRUE, help = "Are the gene and compound data paired?"),
+    make_option(c("--match_data"), type = "logical", default = TRUE, help = "Are the gene and compound data paired?"),
+    make_option(c("--kegg_native"), type = "logical", default = TRUE, help = "Render pathway graph as native KEGG grap? Alternative is the Graphviz layout"),
+    make_option(c("--same_layer"), type = "logical", default = TRUE, help = "Plot on same layer?"),
+    make_option(c("--map_null"), type = "logical", default = TRUE, help = "Map the NULL gene or compound data to pathway?"),
+    make_option(c("--split_group"), type = "logical", default = FALSE, help = "Split node groups into individual nodes?"),
+    make_option(c("--expand_node"), type = "logical", default = FALSE, help = "Expand multiple-gene nodes into single-gene nodes?"),
+    make_option(c("--sign_pos"), type = "character", default = "bottomright", help = "Position of pathview signature")
 )
 
 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
@@ -40,22 +40,22 @@
 print(args)
 
 read_table <- function(fp, header, rownames = 1, colclasses = NA) {
-  table <- read.table(fp, header = header, sep = "\t", row.names = rownames, colClasses = colclasses)
-  # transform to vector if only one column
-  if (dim(table)[2] == 1) {
-    names <- rownames(table)
-    table <- table[, 1]
-    names(table) <- names
-  }
-  return(table)
+    table <- read.table(fp, header = header, sep = "\t", row.names = rownames, colClasses = colclasses)
+    # transform to vector if only one column
+    if (dim(table)[2] == 1) {
+        names <- rownames(table)
+        table <- table[, 1]
+        names(table) <- names
+    }
+    return(table)
 }
 
 get_table <- function(fp, header) {
-  table <- NULL
-  if (!is.null(fp)) {
-    table <- read_table(fp, header, rownames = 1)
-  }
-  return(table)
+    table <- NULL
+    if (!is.null(fp)) {
+        table <- read_table(fp, header, rownames = 1)
+    }
+    return(table)
 }
 
 # load gene_data file
@@ -65,29 +65,30 @@
 cpd_data <- get_table(args$cpd_data, args$cpd_header)
 
 run_pathview <- function(pathway_id) {
-  pathview(
-    pathway.id = pathway_id,
-    gene.data = gene_data,
-    gene.idtype = args$gene_idtype,
-    cpd.data = cpd_data,
-    cpd.idtype = args$cpd_idtype,
-    species = args$species,
-    multi.state = args$multi_state,
-    match.data = args$match_data,
-    kegg.native = args$kegg_native,
-    same.layer = args$same_layer,
-    split.group = args$split_group,
-    expand.node = args$expand_node,
-    sign.pos = args$sign_pos,
-    map.null = args$map_null)
+    pathview(
+        pathway.id = pathway_id,
+        gene.data = gene_data,
+        gene.idtype = args$gene_idtype,
+        cpd.data = cpd_data,
+        cpd.idtype = args$cpd_idtype,
+        species = args$species,
+        multi.state = args$multi_state,
+        match.data = args$match_data,
+        kegg.native = args$kegg_native,
+        same.layer = args$same_layer,
+        split.group = args$split_group,
+        expand.node = args$expand_node,
+        sign.pos = args$sign_pos,
+        map.null = args$map_null
+    )
 }
 
 # get pathway ids
 if (!is.null(args$pathway_id)) {
-  run_pathview(args$pathway_id)
+    run_pathview(args$pathway_id)
 } else {
-  pthws <- read_table(args$pathway_id_fp, args$pathway_id_header, rownames = NULL, colclasses = "character")
-  for (p in pthws) {
-    run_pathview(p)
-  }
+    pthws <- read_table(args$pathway_id_fp, args$pathway_id_header, rownames = NULL, colclasses = "character")
+    for (p in pthws) {
+        run_pathview(p)
+    }
 }