bio-rocker 0.1.02 → 0.1.03

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  metadata.gz: 820871c854cb75ab6a7f98140ea50952dd145fd1
-  data.tar.gz: 83df9b12b3509f02ec4c9dcf1bed4185de817b43
+  metadata.gz: 63b71b4681de7b50aab9c01eb60eed5ce6dc3e7b
+  data.tar.gz: 3ec94f33007a8535f77c2878e32bf51d5bc33395
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+  data.tar.gz: e54a0e01bf15e5b6a054096ac0f8158c7c390fb568d7447cd75c5ffe2e89405ee797ad71afa2667201ef3e9fcf89307d1802e8601abb6737559a81ebce4e770c

data/bin/ROCker

@@ -3,7 +3,7 @@
 # @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
 # @author Luis (Coto) Orellana
 # @license artistic license 2.0
-# @update Feb-09-2015
+# @update Mar-23-2015
 #
 
 require 'rocker'
@@ -128,6 +128,7 @@ opts = OptionParser.new do |opt|
       opt.on(      "--no-transparency", "Do not use (semi-)transparencies."){ |v| o[:transparency] = v }
       opt.on(      "--min-score NUMBER", "Minimum Bit-Score to consider a hit. By default: #{ROCker.default :minscore}"){ |v| o[:minscore]=v.to_f }
       opt.on(      "--stats-impact", "Plot impact on statistics, instead of absolute values per window."){ o[:impact]=true }
+      opt.on(      "--stats-ylim", "Limits of the Y-axis in the bottom panel. By default: '-2,.1' if --stats-impact is set, '50,100' otherwise."){ |v| o[:ylim]=v }
       opt.on("-s", "--subject SBJ1,SBJ2,...", Array,
       	"Plot only information regarding this(ese) subject(s). If multiple, separate by comma. By default, all hits are plotted."){ |v| o[:sbj]=v }
       opt.on("-f", "--plot-format STRING",

data/lib/rocker.rb

@@ -2,7 +2,7 @@
 # @author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>
 # @author Luis (Coto) Orellana
 # @license artistic license 2.0
-# @update Feb-04-2015
+# @update Mar-23-2015
 #
 
 require 'rocker/blasthit'
@@ -433,7 +433,7 @@ class ROCker
 
       puts "Plotting statistics." unless @o[:q]
       data.rrun "par(mar=c(5,4,0,0.5)+.1);"
-      data.rrun "plot(1, t='n', xlim=c(0,#{data.aln.cols}),ylim=c(#{@o[:impact] ? "-2,.1" : "50,100"}),xlab='Alignment position (amino acids)',ylab='Precision',xaxs='i');"
+      data.rrun "plot(1, t='n', xlim=c(0,#{data.aln.cols}),ylim=c(#{@o[:ylim].nil? ? (@o[:impact] ? "-2,.1" : "50,100") : @o[:ylim]}),xlab='Alignment position (amino acids)',ylab='Precision',xaxs='i');"
       if some_thr
 	 sn = data.rrun "100*sum(w$tp)/(sum(w$tp)+sum(w$fn))", :float
 	 sp = data.rrun "100*sum(w$tn)/(sum(w$fp)+sum(w$tn))", :float

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-rocker
 version: !ruby/object:Gem::Version
-  version: 0.1.02
+  version: 0.1.03
 platform: ruby
 authors:
 - Luis (Coto) Orellana