Merge branch 'master' of https://github.com/ding-lab/hotspot3d

Conflicts:
	HotSpot3D-1.0.3.tar.gz
	HotSpot3D-1.0.4.tar.gz
	HotSpot3D-1.1.0.tar.gz
	README.md
	bin/hotspot3d
	dist.ini
	lib/TGI/Mutpro/Main/Cluster.pm

Author: AdamDS

bin/hotspot3d

@@ -70,7 +70,7 @@ sub help_text {
 	return <<HELP        
 Program: hotspot3d - 3D mutation proximity analysis program.
 Version: $VERSION
- Author: Beifang Niu, Adam D Scott, Sohini Sengupta, & John Wallis
+ Author: Beifang Niu, Adam D Scott, Sohini Sengupta, John Wallis & Amila Weerasinghe
 
   Usage: hotspot3d <command> [options]
 

dist.ini

@@ -1,5 +1,5 @@
 name    = HotSpot3D
-author  = Beifang Niu, John Wallis, Adam D Scott, Sohini Sengupta , & Amila Weerasinghe from McDonnell Genome Institute of Washington University at St. Louis
+author  = Beifang Niu, John Wallis, Adam D Scott, Sohini Sengupta, & Amila Weerasinghe from McDonnell Genome Institute of Washington University at St. Louis
 version = 1.1.0
 license = Perl_5
 copyright_holder = McDonnell Genome Institute at Washington University

lib/TGI/Mutpro/Main/BruteForceClustersLines.R

@@ -0,0 +1,20 @@
+#!/usr/bin/env Rscript
+args = commandArgs(trailingOnly=TRUE)
+y = read.table(args[1])
+z = read.table(args[2])
+
+RD<-y[[2]]
+ID<-y[[1]]
+
+x0<-z[[1]] 
+y0<-z[[3]] 
+x1<-z[[2]]+1 
+y1<-z[[3]] 
+
+pdf(args[3],width=23.6,height=13.3)
+par(mar=c(8,5,5,1))
+barplot(RD,names.arg=ID,ylab="Reachabilty Distance (A)",main=paste("Reachability Plot: Epsilon=",args[4],"MinPts=",args[5]),col="Red", border=NA, space=0, las=2, cex.names=0.4)
+segments (x0,y0,x1,y1)
+dev.off()
+
+# args: 1-RD.out, 2-clusters.out, 3-pdf_file_name, 4-epsilon, 5-MinPts, 6-cutoff

lib/TGI/Mutpro/Main/Cluster.pm

@@ -60,6 +60,11 @@ sub new {
     $this->{'weight_header'} = $WEIGHT;
     $this->{'clustering'} = undef;
     $this->{'structure_dependence'} = undef;
+    #$this->{'pairwise_file'} = '3D_Proximity.pairwise';
+    $this->{'Epsilon'} = undef;
+    $this->{'MinPts'} = undef;
+    $this->{'number_of_runs'} = undef;
+    $this->{'probability_cut_off'} = undef;
     bless $this, $class;
     $this->process();
     return $this;
@@ -120,8 +125,12 @@ sub setOptions {
         'clustering=s' => \$this->{'clustering'},		
         'structure-dependence=s' => \$this->{'structure_dependence'},		
         'help' => \$help,
+
+        'Epsilon=f' => \$this->{'Epsilon'},
+        'MinPts=f' => \$this->{'MinPts'},
+        'number-of-runs=f' => \$this->{'number_of_runs'},
+        'probability-cut-off=f' => \$this->{'probability_cut_off'},
     );
-    if ( $help ) { print STDERR help_text(); exit 0; }
     unless( $options ) { die $this->help_text(); }
 	if ( not defined $this->{'clustering'} ) {
 		$this->{'clustering'} = $NETWORK;
@@ -132,9 +141,13 @@ sub setOptions {
 		warn "HotSpot3D::Cluster warning: no structure-dependence option given, setting to default independent\n";
 	}
 	if ( $this->{'clustering'} eq $DENSITY ) {
-		TGI::Mutpro::Main::Density->new();
-		exit;
+		if ( $help ) { print STDERR density_help_text(); exit 0; }
+		else{
+			TGI::Mutpro::Main::Density->new($this);
+			exit;
+		}
 	}
+	if ( $help ) { print STDERR help_text(); exit 0; }
 	if ( not defined $this->{'p_value_cutoff'} ) {
 		if ( not defined $this->{'3d_distance_cutoff'} ) {
 			warn "HotSpot3D::Cluster warning: no pair distance limit given, setting to default p-value cutoff = 0.05\n";
@@ -964,6 +977,26 @@ sub structureDependence {
 	return $ANY;
 }
 
+sub density_help_text{
+    my $this = shift;
+        return <<HELP
+
+Usage: hotspot3d density [options]
+
+                             REQUIRED
+--pairwise-file              3D pairwise data file
+
+                             OPTIONAL
+--Epsilon                    Epsilon value, default: 10
+--MinPts                     MinPts, default: 4
+--number-of-runs             Number of density clustering runs to perform before the cluster membership probability being calculated, default: 10
+--probability-cut-off        Clusters will be formed with variants having at least this probability, default: 100 
+
+--help                       this message
+
+HELP
+}
+
 sub help_text{
     my $this = shift;
         return <<HELP