Merge pull request #24 from brianjohnhaas/devel

added --hclust_method parameter for flexiblity in clustering option choices

Former-commit-id: 26bd1a5

R/inferCNV.R

@@ -233,7 +233,8 @@ create_sep_list <- function(row_count,
 # row, not the first row.
 split_references <- function(average_data,
  ref_obs,
- num_groups){
+ num_groups,
+ hclust_method='complete') {
  logging::loginfo(paste("::split_references:Start", sep=""))
  ret_groups <- list()
  split_groups <- NULL
@@ -269,7 +270,8 @@ split_references <- function(average_data,
  # Get HCLUST
  # Get reference observations only.
  average_reference_obs <- t(average_data[, ref_obs, drop=FALSE])
- hc <- hclust(dist(average_reference_obs))
+
+ hc <- hclust(dist(average_reference_obs), method=hclust_method)
 
  split_groups <- cutree(hc, k=num_groups)
  split_groups <- split_groups[hc$order]
@@ -456,14 +458,16 @@ infer_cnv <- function(data,
  method_bound_vis=NA,
  lower_bound_vis=NA,
  upper_bound_vis=NA,
- ref_subtract_method="by_mean") {
+ ref_subtract_method="by_mean",
+ hclust_method='complete') {
 
  logging::loginfo(paste("::infer_cnv:Start", sep=""))
 
  # Split the reference data into groups if requested
  groups_ref <- split_references(average_data=data, #data_smoothed,
- ref_obs=reference_obs,
- num_groups=num_ref_groups)
+ ref_obs=reference_obs,
+ num_groups=num_ref_groups,
+ hclust_method=hclust_method)
  logging::loginfo(paste("::infer_cnv:split_reference. ",
  "found ",length(groups_ref)," reference groups.",
  sep=""))
@@ -896,6 +900,7 @@ plot_cnv <- function(plot_data,
  contig_cex=1,
  k_obs_groups=1,
  x.center=0,
+ hclust_method='average',
  color_safe_pal=TRUE,
  pdf_filename="infercnv.pdf"){
 
@@ -994,6 +999,7 @@ plot_cnv <- function(plot_data,
  contig_lab_size=contig_cex,
  breaksList=breaksList_t,
  x.center=x.center,
+ hclust_method=hclust_method,
  layout_lmat=force_layout[["lmat"]],
  layout_lhei=force_layout[["lhei"]],
  layout_lwid=force_layout[["lwid"]])
@@ -1049,6 +1055,7 @@ plot_cnv_observations <- function(obs_data,
  cluster_contig=NULL,
  breaksList,
  x.center,
+ hclust_method="average",
  testing=FALSE,
  layout_lmat=NULL,
  layout_lhei=NULL,
@@ -1085,8 +1092,9 @@ plot_cnv_observations <- function(obs_data,
  sep=" ")) 
  }
  }
- # HCL with a inversely weighted euclidean distance.
- obs_hcl <- hclust(dist(obs_data[,hcl_group_indices]),"average")
+ # HCL with a inversely weighted euclidean distance.
+ logging::loginfo(paste("clustering observations via method: ", hclust_method, sep=""))
+ obs_hcl <- hclust(dist(obs_data[,hcl_group_indices]), method=hclust_method)
  obs_dendrogram <- as.dendrogram(obs_hcl)
  write.tree(as.phylo(obs_hcl),
  file=paste(file_base_name, "observations_dendrogram.txt", sep=.Platform$file.sep))

scripts/inferCNV.R

@@ -14,6 +14,7 @@ C_LEVEL_CHOICES <- names(loglevels)
 # Visualization outlier thresholding and bounding method choices
 C_VIS_OUTLIER_CHOICES <- c("average_bound")
 C_REF_SUBTRACT_METHODS <- c("by_mean", "by_quantiles")
+C_HCLUST_METHODS <- c("ward.D", "ward.D2", "single", "complete", "average", "mcquitty", "median", "centroid")
 
 CHR = "chr"
 START = "start"
@@ -71,7 +72,14 @@ check_arguments <- function(arguments){
  paste(C_REF_SUBTRACT_METHODS, collapse=","), sep="") )
  stop("error, must specify acceptable --ref_subtract_method")
  }
-
+
+
+ if (! (arguments$hclust_method %in% C_HCLUST_METHODS) ) {
+ logging::logerror(paste(":: --hclust_method: acceptable values are: ",
+ paste(C_HCLUST_METHODS, collapse=","), sep="") )
+ stop("error, must specify acceptable --hclust_method")
+ }
+
  # Warn that an average of the samples is used in the absence of
  # normal / reference samples
  if (is.null(arguments$reference_observations)){
@@ -292,10 +300,21 @@ pargs <- optparse::add_option(pargs, c("--ref_subtract_method"),
  action="store",
  dest="ref_subtract_method",
  metavar="Reference_Subtraction_Method",
- help=paste("Method used to subtract the reference values from the observations. Valid choices are",
+ help=paste("Method used to subtract the reference values from the observations. Valid choices are: ",
  paste(C_REF_SUBTRACT_METHODS, collapse=", "),
  " [Default %default]"))
 
+pargs <- optparse::add_option(pargs, c("--hclust_method"),
+ type="character",
+ default="complete",
+ action="store",
+ dest="hclust_method",
+ metavar="Hierarchical_Clustering_Method",
+ help=paste("Method used for hierarchical clustering of cells. Valid choices are: ",
+ paste(C_HCLUST_METHODS, collapse=", "),
+ " [Default %default]"))
+
+
 
 pargs <- optparse::add_option(pargs,c("--obs_cluster_contig"),
  type="character",
@@ -542,7 +561,8 @@ ret_list = infercnv::infer_cnv(data=expression_data,
  method_bound_vis=args$bound_method_vis,
  lower_bound_vis=bounds_viz[1],
  upper_bound_vis=bounds_viz[2],
- ref_subtract_method=args$ref_subtract_method)
+ ref_subtract_method=args$ref_subtract_method,
+ hclust_method=args$hclust_method)
 
 # Log output
 logging::loginfo(paste("::infer_cnv:Writing final data to ",
@@ -582,6 +602,7 @@ if (args$plot_steps) {
  ref_groups=ret_list[["REF_GROUPS"]],
  out_dir=args$output_dir,
  color_safe_pal=args$use_color_safe,
+ hclust_method=args$hclust_method,
  title=args$fig_main,
  obs_title=args$obs_main,
  ref_title=args$ref_main)