rbbt-util 5.26.82 → 5.26.83

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: fe65f02a82226b98bff48fc39c862d892d8ffaf1fa68a7b101d7bf5befb67db3
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+  data.tar.gz: cbd3625ce98062162ef323a10a3e991e60947e883171a1c63af25368af2ee076d622ade4321172a59503744acf47db055ec48003a9fa7ed54d12376f5609eca2

data/lib/rbbt/tsv/stream.rb

@@ -21,7 +21,7 @@ module TSV
  
   def self.paste_streams(streams, options = {})
     options = Misc.add_defaults options, :sep => "\t", :sort => true
-    sort, sep, preamble, header, same_fields, fix_flat, all_match = Misc.process_options options, :sort, :sep, :preamble, :header, :same_fields, :fix_flat, :all_match
+    sort, sep, preamble, header, same_fields, fix_flat, all_match, field_prefix = Misc.process_options options, :sort, :sep, :preamble, :header, :same_fields, :fix_flat, :all_match, :field_prefix
 
     out = Misc.open_pipe do |sin|
 
@@ -57,12 +57,20 @@ module TSV
 
       streams = streams.collect do |stream|
         parser = TSV::Parser.new stream, options.dup
+        sfields = parser.fields
+
+        if field_prefix
+          index = streams.index stream
+          prefix = field_prefix[index]
+
+          sfields = sfields.collect{|f| [prefix, f] * ":" }
+        end
 
         lines         << parser.first_line
         empty         << stream               if parser.first_line.nil?
         key_fields    << parser.key_field
-        fields        << parser.fields
-        sizes         << parser.fields.length if parser.fields
+        fields        << sfields
+        sizes         << sfields.length if sfields
         input_options << parser.options
         preambles     << parser.preamble      if preamble and not parser.preamble.empty?
 

data/lib/rbbt/util/R.rb

@@ -40,6 +40,7 @@ source('#{UTIL}');
     Log.debug{"R Script:\n#{ cmd }"}
 
     if monitor
+      #io = CMD.cmd('R --no-save --quiet', options.merge(:in => cmd, :pipe => true, :log => true))
       io = CMD.cmd('R --no-save --quiet', options.merge(:in => cmd, :pipe => true, :log => true))
       while line = io.gets
         case monitor

data/lib/rbbt/util/R/plot.rb

@@ -220,16 +220,12 @@ data = NULL
         options[:R_open] ||= "colClasses=c('character'," + field_classes * ", " + ')' if field_classes.any?
 
         data.R <<-EOF, :plot, options
-  png("#{ filename }", #{ width }, #{ height })
-  { #{script} }
-  dev.off()
+  rbbt.png_plot("#{ filename }", width=#{ width }, height = #{ height }, function(){ #{script} })
   data = NULL
         EOF
       else
         R.run <<-EOF, :plot, options
-  png("#{ filename }", #{ width }, #{ height })
-  { #{script} }
-  dev.off()
+  rbbt.png_plot("#{ filename }", width=#{ width }, height = #{ height }, function(){ #{script} })
         EOF
       end
     end

data/lib/rbbt/util/config.rb

@@ -110,7 +110,7 @@ module Rbbt::Config
       end
     end
 
-    value = priorities.empty? ? default : priorities.collect{|p| p }.sort_by{|p,v| p}.first.last.last
+    value = priorities.empty? ? default : priorities.collect{|p| p }.sort_by{|p,v| p}.first.last.first
     value = false if value == 'false'
 
     Log.debug "Value #{value.inspect} for config key '#{ key }': #{tokens * ", "}"

data/lib/rbbt/workflow.rb

@@ -422,7 +422,7 @@ module Workflow
     task_inputs = task_info[:inputs]
     persist_inputs = inputs.values_at(*task_inputs)
     persist_inputs += inputs.values_at(*inputs.keys.select{|k| String === k && k.include?("#") }.sort)
-    Persist.memory("STEP", :taskname => taskname, :jobname => jobname, :inputs => persist_inputs, :repo => step_cache) do
+    Persist.memory("STEP", :workflow => self.to_s, :taskname => taskname, :jobname => jobname, :inputs => persist_inputs, :repo => step_cache) do
       __job(taskname, jobname, inputs)
     end
   end

data/share/Rlib/util.R

@@ -563,14 +563,22 @@ rbbt.get.modes <- function(x,bw = NULL,spar = NULL) {
 #{{{ PLOTS
 
 rbbt.png_plot <- function(filename, p, width=500, height=500, ...){
-    png(filename=filename, width=width, height=height, ...);
-    eval(parse(text=p));
+    png(filename=filename, width=width, height=height, type='cairo', ...);
+    if (is.function(p)) {
+      p()
+    }else{
+      eval(parse(text=p));
+    }
     dev.off()
 }
 
 rbbt.tiff_plot <- function(filename, p, width=500, height=500, ...){
     tiff(filename=filename, width=width, height=height, ...);
-    eval(parse(text=p));
+    if (is.function(p)) {
+      p()
+    }else{
+      eval(parse(text=p));
+    }
     dev.off()
 }
 
@@ -713,9 +721,21 @@ rbbt.plot.matrix <- function(x, ...){
     layout(1);
 }
 
+rbbt.plot.set_colors <- function(size, set="Set1"){
+  rbbt.require('RColorBrewer')
+  return(brewer.pal(size, set))
+}
+
 # Adapted from: https://rstudio-pubs-static.s3.amazonaws.com/13301_6641d73cfac741a59c0a851feb99e98b.html
-rbbt.plot.venn <- function(data, a, ...) {
+rbbt.plot.venn <- function(data, a=NULL, category=NULL, fill=NULL, ...) {
     rbbt.require('VennDiagram')
+
+    if (is.null(a)){ 
+      a = names(data); 
+      category = a; 
+      fill=rbbt.plot.set_colors(dim(data)[2], "Set3")
+    }
+
     group.matches <- function(data, fields) {
         sub = data
         for (i in 1:length(fields)) {
@@ -725,20 +745,20 @@ rbbt.plot.venn <- function(data, a, ...) {
     }
 
     if (length(a) == 1) {
-        out <- draw.single.venn(group.matches(data, a), ...)
+        out <- draw.single.venn(group.matches(data, a), category=category, fill=fill, ...)
     }
     if (length(a) == 2) {
-        out <- draw.pairwise.venn(group.matches(data, a[1]), group.matches(data, a[2]), group.matches(data, a[1:2]), ...)
+        out <- draw.pairwise.venn(group.matches(data, a[1]), group.matches(data, a[2]), group.matches(data, a[1:2]), category=category, fill=fill, ...)
     }
     if (length(a) == 3) {
         out <- draw.triple.venn(group.matches(data, a[1]), group.matches(data, a[2]), group.matches(data, a[3]), group.matches(data, a[1:2]), 
-            group.matches(data, a[2:3]), group.matches(data, a[c(1, 3)]), group.matches(data, a), ...)
+            group.matches(data, a[2:3]), group.matches(data, a[c(1, 3)]), group.matches(data, a), category=category, fill=fill, ...)
     }
     if (length(a) == 4) {
         out <- draw.quad.venn(group.matches(data, a[1]), group.matches(data, a[2]), group.matches(data, a[3]), group.matches(data, a[4]), 
             group.matches(data, a[1:2]), group.matches(data, a[c(1, 3)]), group.matches(data, a[c(1, 4)]), group.matches(data, a[2:3]), 
             group.matches(data, a[c(2, 4)]), group.matches(data, a[3:4]), group.matches(data, a[1:3]), group.matches(data, a[c(1, 2, 
-                4)]), group.matches(data, a[c(1, 3, 4)]), group.matches(data, a[2:4]), group.matches(data, a), ...)
+                4)]), group.matches(data, a[c(1, 3, 4)]), group.matches(data, a[2:4]), group.matches(data, a), category=category, fill=fill, ...)
     }
     if (length(a) == 5) {
         out <- draw.quintuple.venn(
@@ -755,7 +775,7 @@ rbbt.plot.venn <- function(data, a, ...) {
             group.matches(data, a[c(3, 4, 5)]),
             group.matches(data, a[c(1, 2, 3, 4)]),group.matches(data, a[c(1, 2, 3, 5)]),group.matches(data, a[c(1, 2, 4, 5)]),group.matches(data, a[c(1, 3, 4, 5)]),group.matches(data, a[c(2, 3, 4, 5)]),
             group.matches(data, a),
-            ...)
+            category=category, fill=fill, ...)
 
     }
     if (!exists("out")) 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.26.82
+  version: 5.26.83
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-10-03 00:00:00.000000000 Z
+date: 2019-10-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake