--- a/CEMiTool.R	Mon Oct 10 16:55:19 2022 +0000
+++ b/CEMiTool.R	Mon Aug 19 10:47:14 2024 +0000
@@ -4,11 +4,11 @@
 library(getopt, quietly = TRUE, warn.conflicts = FALSE)
 # setup R error handling to go to stderr
 options(
-  show.error.messages = FALSE,
-  error = function() {
-    cat(geterrmessage(), file = stderr())
-    q("no", 1, FALSE)
-  }
+    show.error.messages = FALSE,
+    error = function() {
+        cat(geterrmessage(), file = stderr())
+        q("no", 1, FALSE)
+    }
 )
 
 # we need that to not crash galaxy with an UTF8 error on German LC settings.
@@ -23,133 +23,139 @@
 
 # Get options, using the spec as defined by the enclosed list.
 # Read the options from the default: commandArgs(TRUE).
-spec <- matrix(c(
-  "expressionMatrix", "M", 1, "character",
-  "sampleAnnotation", "A", 2, "character",
-  "pathwayList", "P", 2, "character",
-  "interactions", "I", 2, "character",
-  "filter", "f", 1, "logical",
-  "filter_pval", "i", 1, "numeric",
-  "apply_vst", "a", 1, "logical",
-  "n_genes", "n", 1, "integer",
-  "eps", "e", 1, "numeric",
-  "cor_method", "c", 1, "character",
-  "cor_function", "y", 1, "character",
-  "network_type", "x", 1, "character",
-  "tom_type", "t", 1, "character",
-  "merge_similar", "m", 1, "logical",
-  "rank_method", "r", 1, "character",
-  "min_ngen", "g", 1, "integer",
-  "diss_thresh", "d", 1, "numeric",
-  "center_func", "h", 1, "character",
-  "ora_pval", "o", 1, "numeric",
-  "gsea_scale", "l", 1, "logical",
-  "gsea_min_size", "w", 1, "integer",
-  "gsea_max_size", "z", 1, "integer",
-  "sample_column_name", "v", 1, "character"),
-byrow = TRUE, ncol = 4
+spec <- matrix(
+    c(
+        "expressionMatrix", "M", 1, "character",
+        "sampleAnnotation", "A", 2, "character",
+        "pathwayList", "P", 2, "character",
+        "interactions", "I", 2, "character",
+        "set_beta", "B", 1, "integer",
+        "filter", "f", 1, "logical",
+        "filter_pval", "i", 1, "numeric",
+        "apply_vst", "a", 1, "logical",
+        "n_genes", "n", 1, "integer",
+        "eps", "e", 1, "numeric",
+        "cor_method", "c", 1, "character",
+        "cor_function", "y", 1, "character",
+        "network_type", "x", 1, "character",
+        "tom_type", "t", 1, "character",
+        "merge_similar", "m", 1, "logical",
+        "rank_method", "r", 1, "character",
+        "min_ngen", "g", 1, "integer",
+        "diss_thresh", "d", 1, "numeric",
+        "center_func", "h", 1, "character",
+        "ora_pval", "o", 1, "numeric",
+        "gsea_scale", "l", 1, "logical",
+        "gsea_min_size", "w", 1, "integer",
+        "gsea_max_size", "z", 1, "integer",
+        "sample_column_name", "v", 1, "character"
+    ),
+    byrow = TRUE, ncol = 4
 )
 
 opt <- getopt(spec)
 counts <- read.table(
-  opt$expressionMatrix,
-  header = TRUE,
-  sep = "\t",
-  strip.white = TRUE,
-  stringsAsFactors = FALSE,
-  check.names = FALSE
+    opt$expressionMatrix,
+    header = TRUE,
+    sep = "\t",
+    strip.white = TRUE,
+    stringsAsFactors = FALSE,
+    check.names = FALSE
 )
 
 
 # Run CEMiTool
 
 if (is.null(opt$sampleAnnotation)) {
-  cem <- cemitool(
-    counts,
-    filter = opt$filter,
-    filter_pval = opt$filter_pval,
-    apply_vst = opt$apply_vst,
-    n_genes = opt$n_genes,
-    eps = opt$eps,
-    cor_method = opt$cor_method,
-    cor_function = opt$cor_function,
-    network_type = opt$network_type,
-    tom_type = opt$tom_type,
-    merge_similar = opt$merge_similar,
-    min_ngen = opt$min_ngen,
-    diss_thresh = opt$diss_thresh,
-    center_func = opt$center_func,
-    verbose = TRUE,
-    ora_pval = opt$ora_pval
-  )
+    cem <- cemitool(
+        counts,
+        filter = opt$filter,
+        filter_pval = opt$filter_pval,
+        apply_vst = opt$apply_vst,
+        n_genes = opt$n_genes,
+        eps = opt$eps,
+        cor_method = opt$cor_method,
+        cor_function = opt$cor_function,
+        network_type = opt$network_type,
+        tom_type = opt$tom_type,
+        merge_similar = opt$merge_similar,
+        min_ngen = opt$min_ngen,
+        diss_thresh = opt$diss_thresh,
+        center_func = opt$center_func,
+        verbose = TRUE,
+        ora_pval = opt$ora_pval,
+        set_beta = opt$set_beta
+    )
 } else {
-  annotation <- read.table(
-    opt$sampleAnnotation,
-    header = TRUE,
-    sep = "\t",
-    strip.white = TRUE,
-    stringsAsFactors = FALSE,
-    check.names = FALSE
-  )
-  cem <- cemitool(
-    counts,
-    annotation,
-    filter = opt$filter,
-    filter_pval = opt$filter_pval,
-    apply_vst = opt$apply_vst,
-    n_genes = opt$n_genes,
-    eps = opt$eps,
-    cor_method = opt$cor_method,
-    cor_function = opt$cor_function,
-    network_type = opt$network_type,
-    tom_type = opt$tom_type,
-    merge_similar = opt$merge_similar,
-    min_ngen = opt$min_ngen,
-    diss_thresh = opt$diss_thresh,
-    center_func = opt$center_func,
-    verbose = TRUE,
-    ora_pval = opt$ora_pval,
-    sample_name_column = opt$sample_column_name,
-    class_column = "Class",
-    order_by_class = TRUE
-  )
-  cem <- mod_gsea(
-    cem,
-    gsea_scale = opt$gsea_scale,
-    gsea_min_size = opt$gsea_min_size,
-    gsea_max_size = opt$gsea_max_size,
-    rank_method = opt$rank_method
-)
-  cem <- plot_gsea(cem)
+    annotation <- read.table(
+        opt$sampleAnnotation,
+        header = TRUE,
+        sep = "\t",
+        strip.white = TRUE,
+        stringsAsFactors = FALSE,
+        check.names = FALSE
+    )
+    cem <- cemitool(
+        counts,
+        annotation,
+        filter = opt$filter,
+        filter_pval = opt$filter_pval,
+        apply_vst = opt$apply_vst,
+        n_genes = opt$n_genes,
+        eps = opt$eps,
+        cor_method = opt$cor_method,
+        cor_function = opt$cor_function,
+        network_type = opt$network_type,
+        tom_type = opt$tom_type,
+        merge_similar = opt$merge_similar,
+        min_ngen = opt$min_ngen,
+        diss_thresh = opt$diss_thresh,
+        center_func = opt$center_func,
+        verbose = TRUE,
+        ora_pval = opt$ora_pval,
+        sample_name_column = opt$sample_column_name,
+        class_column = "Class",
+        order_by_class = TRUE
+    )
+    cem <- mod_gsea(
+        cem,
+        gsea_scale = opt$gsea_scale,
+        gsea_min_size = opt$gsea_min_size,
+        gsea_max_size = opt$gsea_max_size,
+        rank_method = opt$rank_method
+    )
+    cem <- plot_gsea(cem)
 }
 
 if (!is.null(opt$pathwayList)) {
-  gmt_in <- read_gmt(opt$pathwayList)
-  cem <- mod_ora(cem, gmt_in)
-  cem <- plot_ora(cem)
+    gmt_in <- read_gmt(opt$pathwayList)
+    cem <- mod_ora(cem, gmt_in)
+    cem <- plot_ora(cem)
 }
 
 if (!is.null(opt$interactions)) {
-  interactions <- read.table(
-    opt$interactions,
-    header = TRUE,
-    sep = "\t",
-    strip.white = TRUE,
-    stringsAsFactors = FALSE,
-    check.names = FALSE
-  )
-  interactions_data(cem) <- interactions # add interactions
-  cem <- plot_interactions(cem)
+    interactions <- read.table(
+        opt$interactions,
+        header = TRUE,
+        sep = "\t",
+        strip.white = TRUE,
+        stringsAsFactors = FALSE,
+        check.names = FALSE
+    )
+    interactions_data(cem) <- interactions # add interactions
+    cem <- plot_interactions(cem)
 }
 
 ## Write analysis results into files
 write_files(cem,
-            directory = "./Tables",
-            force = TRUE)
+    directory = "./Tables",
+    force = TRUE
+)
 
 generate_report(cem)
 
 save_plots(cem,
-           value = "all",
-           directory = "./Plots",
-           force = TRUE)
+    value = "all",
+    directory = "./Plots",
+    force = TRUE
+)