vienna_rna 0.5.3 → 0.5.4

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -1,3 +1,6 @@
+ViennaRna
+------------------------
+
 A simple gem for facilitating bindings to the ViennaRNA package (http://www.tbi.univie.ac.at/~ivo/RNA/). Note that this gem makes no effort to build and install the ViennaRNA suite locally at this time, and instead relies on its presence on the host machine. Leverages the BioRuby gem (http://bioruby.open-bio.org/) libraries for file parsing.
 
 Simple use case:
@@ -16,4 +19,4 @@ Simple use case:
     > mfe_rna = RNA("CCUCGAGGGGAACCCGAAAGGGACCCGAGAGG").run(:fold).mfe_rna
     #=> echo CCUCGAGGGGAACCCGAAAGGGACCCGAGAGG | rnafold --noPS
     #=> Total runtime: 0.013 sec.
-    #=> #<ViennaRna::Rna CCUCGAGGGGAACCCGAAAG... ((((..(((...(((....) [truncated]>
+    #=> #<ViennaRna::Rna CCUCGAGGGGAACCCGAAAG... ((((..(((...(((....) [truncated]>

data/lib/vienna_rna/modules/graphing.rb

@@ -4,17 +4,33 @@ module ViennaRna
       class << self
         def graph(&block)
           begin
-            (yield r_instance = RinRuby.new).tap { ap r_instance.close }
+            (yield (r_instance = RinRuby.new)).tap { r_instance.close }
           rescue RuntimeError => e
             raise unless e.message == "Unsupported data type on R's end"
           end
         end
 
-        def pdf(string)
+        def line_graph(data, title: nil, type: "l", x_label: "Independent", y_label: "Dependent", filename: false)
+          graph do |r|
+            r.assign("line_graph.x", data.map(&:first))
+            r.assign("line_graph.y", data.map(&:last))
 
+            if filename && (filename = filename.end_with?(".pdf") ? filename : filename + ".pdf")
+              r.eval <<-STR
+                pdf("#{filename}", 6, 6)
+                plot(line_graph.x, line_graph.y, xlab = "#{x_label}", ylab = "#{y_label}", main = "#{title || 'Line Graph'}", type = "#{type}")
+                dev.off()
+              STR
+            else
+              r.eval <<-STR
+                quartz("Histogram", 6, 6)
+                plot(line_graph.x, line_graph.y, xlab = "#{x_label}", ylab = "#{y_label}", main = "#{title || 'Line Graph'}", type = "#{type}")
+              STR
+            end
+          end
         end
         
-        def histogram(data, title: nil, x_label: "Bins", bin_size: 1, filename: false)
+        def histogram(data, title: nil, x_label: "Bins", bin_size: 1, relative: false, filename: false)
           half     = bin_size / 2.0
           range    = Range.new((data.min - half).floor, (data.max + half).ceil)
           breaks   = (range.min + half).step(range.max + half, bin_size).to_a
@@ -26,13 +42,13 @@ module ViennaRna
             if filename && (filename = filename.end_with?(".pdf") ? filename : filename + ".pdf")
               r.eval <<-STR
                 pdf("#{filename}", 6, 6)
-                hist(histogram.data, breaks = histogram.breaks, xlab = "#{x_label} (width: #{bin_size})", main = "#{title || 'Histogram'}")
+                hist(histogram.data, breaks = histogram.breaks, xlab = "#{x_label} (width: #{bin_size})", main = "#{title || 'Histogram'}", freq = #{relative ? 'FALSE' : 'TRUE'})
                 dev.off()
               STR
             else
               r.eval <<-STR
                 quartz("Histogram", 6, 6)
-                hist(histogram.data, breaks = histogram.breaks, xlab = "#{x_label} (width: #{bin_size})", main = "#{title || 'Histogram'}")
+                hist(histogram.data, breaks = histogram.breaks, xlab = "#{x_label} (width: #{bin_size})", main = "#{title || 'Histogram'}", freq = #{relative ? 'FALSE' : 'TRUE'})
               STR
             end
           end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: vienna_rna
 version: !ruby/object:Gem::Version
-  version: 0.5.3
+  version: 0.5.4
 platform: ruby
 authors:
 - Evan Senter
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-06-20 00:00:00.000000000 Z
+date: 2013-06-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio