v0.3.2

#9

README.md

@@ -1,11 +1,12 @@
-# YouPlot
+![Logo](https://user-images.githubusercontent.com/5798442/102004318-ec89d280-3d52-11eb-8608-d890b42593f1.png)
 
 ![Build Status](https://github.com/kojix2/youplot/workflows/test/badge.svg)
 [![Gem Version](https://badge.fury.io/rb/youplot.svg)](https://badge.fury.io/rb/youplot)
 [![Docs Latest](https://img.shields.io/badge/docs-latest-blue.svg)](https://rubydoc.info/gems/youplot)
 [![The MIT License](https://img.shields.io/badge/license-MIT-blue.svg)](LICENSE.txt)
+[![DOI](https://zenodo.org/badge/283230219.svg)](https://zenodo.org/badge/latestdoi/283230219)
 
-Create ASCII charts on the terminal with data from standard streams in the pipeline. 
+YouPlot is a command line tool for Unicode Plotting working with data from standard stream.
 
 :bar_chart: Powered by [UnicodePlot](https://github.com/red-data-tools/unicode_plot.rb)
 
@@ -15,16 +16,22 @@ Create ASCII charts on the terminal with data from standard streams in the pipel
 gem install youplot
 ```
 
-## Screenshots
+## Quick Start
 
-**histogram**
+`cat data.tsv | uplot <command> [options]`
+
+### barplot
 
 ```sh
-ruby -r numo/narray -e "puts Numo::DFloat.new(1000).rand_norm.to_a" \
-  | uplot hist --nbins 15
+curl -sL https://git.io/ISLANDScsv \
+| sort -nk2 -t, \
+| tail -n15 \
+| uplot bar -d, -t "Areas of the World's Major Landmasses"
 ```
 
-<img src="https://i.imgur.com/wpsoGJq.png" width="75%" height="75%">
+![barplot](https://user-images.githubusercontent.com/5798442/101999903-d36a2d00-3d24-11eb-9361-b89116f44122.png)
+
+### histogram
 
 ```sh
 echo -e "from numpy import random;" \
@@ -33,91 +40,119 @@ echo -e "from numpy import random;" \
 | python \
 | uplot hist --nbins 20
 ```
+![histogram](https://user-images.githubusercontent.com/5798442/101999820-21cafc00-3d24-11eb-86db-e410d19b07df.png)
 
-<img src="https://i.imgur.com/97R2MQx.png" width="75%" height="75%">
-
-**scatter**
+### lineplot
 
 ```sh
-curl -s https://raw.githubusercontent.com/uiuc-cse/data-fa14/gh-pages/data/iris.csv \
-| cut -f1-4 -d, \
-| uplot scatter -H -d, -t IRIS
+curl -sL https://git.io/AirPassengers \
+| cut -f2,3 -d, \
+| uplot line -d, -w 50 -h 15 -t AirPassengers --xlim 1950,1960 --ylim 0,600
 ```
 
-<img src="https://i.imgur.com/STX7bFT.png" width="75%" height="75%">
+![lineplot](https://user-images.githubusercontent.com/5798442/101999825-24c5ec80-3d24-11eb-99f4-c642e8d221bc.png)
 
-**line**
+### scatter
 
 ```sh
-curl -s https://www.mhlw.go.jp/content/pcr_positive_daily.csv \
-| cut -f2 -d, \
-| uplot line -w 50 -h 15 -t 'PCR positive tests' --xlabel Date --ylabel number
+curl -sL https://git.io/IRIStsv \
+| cut -f1-4 \
+| uplot scatter -H -t IRIS
 ```
 
-<img src="https://i.imgur.com/PVl5dsa.png" width="75%" height="75%">
+![scatter](https://user-images.githubusercontent.com/5798442/101999827-27284680-3d24-11eb-9903-551857eaa69c.png)
 
-**box**
+### density
 
 ```sh
-curl -s https://raw.githubusercontent.com/uiuc-cse/data-fa14/gh-pages/data/iris.csv \
-| cut -f1-4 -d, \
-| uplot box -H -d, -t IRIS
+curl -sL https://git.io/IRIStsv \
+| cut -f1-4 \
+| uplot density -H -t IRIS
 ```
 
-<img src="https://i.imgur.com/sNI4SmN.png" width="75%" height="75%">
+![density](https://user-images.githubusercontent.com/5798442/101999828-2abbcd80-3d24-11eb-902c-2f44266fa6ae.png)
 
-**colors**
+### boxplot
 
 ```sh
-uplot colors
+curl -sL https://git.io/IRIStsv \
+| cut -f1-4 \
+| uplot boxplot -H -t IRIS
 ```
 
-<img src="https://i.imgur.com/LxyHQsz.png">
+![boxplot](https://user-images.githubusercontent.com/5798442/101999830-2e4f5480-3d24-11eb-8891-728c18bf5b35.png)
+
+### count
+
+In this example, YouPlot counts the number of chromosomes where the gene is located from the human gene annotation file and create a bar chart. The human gene annotation file can be downloaded from the following website.
+
+* https://www.gencodegenes.org/human/
+
+```sh
+cat gencode.v35.annotation.gff3 \
+| grep -v '#' | grep 'gene' | cut -f1 | \
+ uplot count -t "The number of human gene annotations per chromosome"  -c blue
+```
+
+![count](https://user-images.githubusercontent.com/5798442/101999832-30b1ae80-3d24-11eb-96fe-e5000bed1f5c.png)
+
+Note: `count` is not very fast because it runs in a Ruby script.
+This is fine if the data is small, that is, in most cases. However, if you want to visualize huge data, it is faster to use a combination of common Unix commands as shown below.
+
+```sh
+cat gencode.v35.annotation.gff3 | grep -v '#' | grep 'gene' | cut -f1 \
+|sort | uniq -c | sort -nrk2 | awk '{print $2,$1}' \
+| uplot bar -d ' ' -t "The number of human gene annotations per chromosome"  -c blue
+```
 
 ## Usage
 
-`uplot --help`
+### Why YouPlot?
 
-```
-Program: YouPlot (Tools for plotting on the terminal)
-Version: 0.2.7 (using UnicodePlot 0.0.4)
-Source:  https://github.com/kojix2/youplot
+Wouldn't it be a bit of pain to have to run R, Python, Julia, gnuplot or whatever REPL just to check your data?
+YouPlot is a command line tool for this purpose. With YouPlot, you can continue working without leaving your terminal and shell. 
 
-Usage:   uplot <command> [options] <in.tsv>
+### how to use YouPlot?
 
-Commands:
-    barplot    bar
-    histogram  hist
-    lineplot   line
-    lineplots  lines
-    scatter    s
-    density    d
-    boxplot    box
-    colors                   show the list of available colors
+`uplot` is the shortened form of `youplot`. You can use either.
 
-    count      c             baplot based on the number of occurrences
-                             (slower than `sort | uniq -c | sort -n -k1`)
+|                                   |                                                |
+|-----------------------------------|------------------------------------------------|
+| Reads data from standard input    | `cat data.tsv \| uplot <command> [options]`    |
+| Reads data from files             | `uplot <command> [options] data.tsv ...`       |
+| Outputs data from stdin to stdout | `pipeline1 \| uplot <command> -O \| pipeline2` |
 
-Options:
-    -O, --pass [VAL]         file to output standard input data to [stdout]
-                             for inserting YouPlot in the middle of Unix pipes
-    -o, --output VAL         file to output results to [stderr]
-    -d, --delimiter VAL      use DELIM instead of TAB for field delimiter
-    -H, --headers            specify that the input has header row
-    -T, --transpose          transpose the axes of the input data
-    -t, --title VAL          print string on the top of plot
-    -x, --xlabel VAL         print string on the bottom of the plot
-    -y, --ylabel VAL         print string on the far left of the plot
-    -w, --width VAL          number of characters per row
-    -h, --height VAL         number of rows
-    -b, --border VAL         specify the style of the bounding box
-    -m, --margin VAL         number of spaces to the left of the plot
-    -p, --padding VAL        space of the left and right of the plot
-    -c, --color VAL          color of the drawing
-        --[no-]labels        hide the labels
-        --fmt VAL            xyxy : header is like x1, y1, x2, y2, x3, y3...
-                             xyy  : header is like x, y1, y2, y2, y3...
-```
+### Where to output the plot?
+
+By default, the plot is output to *standard error output*. 
+The output file or stream for the plot can be specified with the `-o` option.
+
+### Where to output the input data?
+
+By default, the input data is not output anywhere.
+The `-O` option, with no arguments, outputs the input data directly to the standard output. This is useful when passing data to a subsequent pipeline.
+
+### What types of plots are available?
+
+The following sub-commands are available
+
+| command   | short | how it works                           |
+|-----------|-------|----------------------------------------|
+| barplot   | bar   | draw a horizontal barplot              |
+| histogram | hist  | draw a horizontal histogram            |
+| lineplot  | line  | draw a line chart                      |
+| lineplots | lines | draw a line chart with multiple series |
+| scatter   | s     | draw a scatter plot                    |
+| density   | d     | draw a density plot                    |
+| boxplot   | box   | draw a horizontal boxplot              |
+
+See Quick Start for `count`.
+
+| command   | short | how it works                                             |
+|-----------|-------|----------------------------------------------------------|
+| count     | c     |  draw a baplot based on the number of occurrences (slow) |
+
+### How to view detailed command line options
 
 Use `--help` to print command-specific options.
 
@@ -135,13 +170,29 @@ Options:
 ...
 ```
 
-## Development
+### How to view the list of available colors?
 
-Let's keep it simple.
+```sh
+uplot colors
+```
 
 ## Contributing
 
-Bug reports and pull requests are welcome on GitHub at [https://github.com/kojix2/youplot](https://github.com/kojix2/youplot).
+* [Report bugs](https://github.com/kojix2/youplot/issues)
+* Fix bugs and [submit pull requests](https://github.com/kojix2/youplot/pulls)
+* Write, clarify, or fix documentation
+* Suggest or add new features
+
+
+### Development
+
+```sh
+git clone https://github.com/your_name/GR.rb # Clone the Git repo
+cd GR.rb
+bundle install             # Install the gem dependencies
+bundle exec rake test      # Run the test
+bundle exec rake install   # Installation from source code
+```
 
 ## License
 

lib/youplot.rb

@@ -2,7 +2,7 @@
 
 require 'unicode_plot'
 require 'youplot/version'
-require 'youplot/preprocessing'
+require 'youplot/dsv_reader'
 require 'youplot/command'
 
 module YouPlot

lib/youplot/backends/processing.rb

@@ -0,0 +1,24 @@
+# frozen_string_literal: true
+
+module YouPlot
+  # plotting functions.
+  module Backends
+    module Processing
+      module_function
+
+      def count_values(arr)
+        # tally was added in Ruby 2.7
+        if Enumerable.method_defined? :tally
+          arr.tally
+        else
+          # https://github.com/marcandre/backports
+          arr.each_with_object(Hash.new(0)) { |item, res| res[item] += 1 }
+             .tap { |h| h.default = nil }
+        end
+          .sort { |a, b| a[1] <=> b[1] }
+          .reverse
+          .transpose
+      end
+    end
+  end
+end

lib/youplot/backends/unicode_plot_backend.rb

@@ -1,5 +1,6 @@
 # frozen_string_literal: true
 
+require_relative 'processing'
 require 'unicode_plot'
 
 module YouPlot
@@ -8,23 +9,33 @@ module YouPlot
     module UnicodePlotBackend
       module_function
 
-      def barplot(data, params, count: false)
+      def barplot(data, params, fmt = nil, count: false)
         headers = data.headers
         series = data.series
         # `uplot count`
         if count
-          series = Preprocessing.count_values(series[0])
+          series = Processing.count_values(series[0])
           params.title = headers[0] if headers
         end
         if series.size == 1
-          # If there is only one series, use the line number for label.
+          # If there is only one series.use the line number for label.
           params.title ||= headers[0] if headers
           labels = Array.new(series[0].size) { |i| (i + 1).to_s }
           values = series[0].map(&:to_f)
         else
-          params.title ||= headers[1] if headers
-          labels = series[0]
-          values = series[1].map(&:to_f)
+          # If there are 2 or more series...
+          if fmt == 'yx'
+            # assume that the first 2 series are the y and x series respectively.
+            x_col = 1
+            y_col = 0
+          else
+            # assume that the first 2 series are the x and y series respectively.
+            x_col = 0
+            y_col = 1
+          end
+          params.title ||= headers[y_col] if headers
+          labels = series[x_col]
+          values = series[y_col].map(&:to_f)
         end
         UnicodePlot.barplot(labels, values, **params.to_hc)
       end
@@ -37,7 +48,7 @@ module YouPlot
         UnicodePlot.histogram(values, **params.to_hc)
       end
 
-      def line(data, params)
+      def line(data, params, fmt = nil)
         headers = data.headers
         series = data.series
         if series.size == 1
@@ -46,14 +57,22 @@ module YouPlot
           y = series[0].map(&:to_f)
           UnicodePlot.lineplot(y, **params.to_hc)
         else
-          # If there are 2 or more series,
-          # assume that the first 2 series are the x and y series respectively.
-          if headers
-            params.xlabel ||= headers[0]
-            params.ylabel ||= headers[1]
+          # If there are 2 or more series...
+          if fmt == 'yx'
+            # assume that the first 2 series are the y and x series respectively.
+            x_col = 1
+            y_col = 0
+          else
+            # assume that the first 2 series are the x and y series respectively.
+            x_col = 0
+            y_col = 1
           end
-          x = series[0].map(&:to_f)
-          y = series[1].map(&:to_f)
+          if headers
+            params.xlabel ||= headers[x_col]
+            params.ylabel ||= headers[y_col]
+          end
+          x = series[x_col].map(&:to_f)
+          y = series[y_col].map(&:to_f)
           UnicodePlot.lineplot(x, y, **params.to_hc)
         end
       end
@@ -102,6 +121,8 @@ module YouPlot
           plot_xyy(data, method1, params)
         when 'xyxy'
           plot_xyxy(data, method1, params)
+        when 'yx'
+          raise "Incorrect format: #{fmt}"
         else
           raise "Unknown format: #{fmt}"
         end
@@ -131,17 +152,23 @@ module YouPlot
       end
 
       def colors(color_names = false)
+        # FIXME
+        s = String.new
         UnicodePlot::StyledPrinter::TEXT_COLORS.each do |k, v|
-          print v
-          print k
+          s << v
+          s << k.to_s
           unless color_names
-            print "\t"
-            print '  ●'
+            s << "\t"
+            s << '  ●'
           end
-          print "\033[0m"
-          print "\t"
+          s << "\033[0m"
+          s << "\t"
         end
-        puts
+        s << "\n"
+        def s.render(obj)
+          obj.print(self)
+        end
+        s
       end
 
       def check_series_size(data, fmt)

lib/youplot/command.rb

@@ -1,6 +1,6 @@
 # frozen_string_literal: true
 
-require_relative 'preprocessing'
+require_relative 'dsv_reader'
 require_relative 'command/parser'
 
 # FIXME
@@ -10,77 +10,99 @@ module YouPlot
   Data = Struct.new(:headers, :series)
 
   class Command
-    attr_accessor :params
-    attr_reader :data, :fmt, :parser
+    attr_accessor :command, :params, :options
+    attr_reader :data, :parser
 
     def initialize(argv = ARGV)
       @argv    = argv
-      @params  = Params.new
       @parser  = Parser.new
+      @command = nil
+      @params  = nil
+      @options = nil
       @backend = YouPlot::Backends::UnicodePlotBackend
     end
 
     def run
       parser.parse_options(@argv)
-      command   = parser.command
-      params    = parser.params
-      delimiter = parser.delimiter
-      transpose = parser.transpose
-      headers   = parser.headers
-      pass      = parser.pass
-      output    = parser.output
-      fmt       = parser.fmt
-      @debug    = parser.debug
+      @command ||= parser.command
+      @options ||= parser.options
+      @params  ||= parser.params
 
-      if command == :colors
-        @backend.colors(parser.color_names)
-        exit
+      if %i[colors color colours colour].include? @command
+        plot = create_plot
+        output_plot(plot)
+      else
+        # Sometimes the input file does not end with a newline code.
+        while (input = Kernel.gets(nil))
+          main(input)
+        end
       end
+    end
 
-      # Sometimes the input file does not end with a newline code.
-      while (input = Kernel.gets(nil))
-        input.freeze
-        @data = Preprocessing.input(input, delimiter, headers, transpose)
-        pp @data if @debug
-        plot = case command
-               when :bar, :barplot
-                 @backend.barplot(data, params)
-               when :count, :c
-                 @backend.barplot(data, params, count: true)
-               when :hist, :histogram
-                 @backend.histogram(data, params)
-               when :line, :lineplot
-                 @backend.line(data, params)
-               when :lines, :lineplots
-                 @backend.lines(data, params, fmt)
-               when :scatter, :s
-                 @backend.scatter(data, params, fmt)
-               when :density, :d
-                 @backend.density(data, params, fmt)
-               when :box, :boxplot
-                 @backend.boxplot(data, params)
-               else
-                 raise "unrecognized plot_type: #{command}"
-               end
+    private
 
-        case output
-        when IO
-          plot.render(output)
-        else
-          File.open(output, 'w') do |f|
-            plot.render(f)
+    def main(input)
+      output_data(input)
+
+      @data = read_dsv(input)
+
+      pp @data if options[:debug]
+
+      plot = create_plot
+      output_plot(plot)
+    end
+
+    def read_dsv(input)
+      input = input.dup.force_encoding(options[:encoding]).encode('utf-8') if options[:encoding]
+      DSVReader.input(input, options[:delimiter], options[:headers], options[:transpose])
+    end
+
+    def create_plot
+      case command
+      when :bar, :barplot
+        @backend.barplot(data, params, options[:fmt])
+      when :count, :c
+        @backend.barplot(data, params, count: true)
+      when :hist, :histogram
+        @backend.histogram(data, params)
+      when :line, :lineplot
+        @backend.line(data, params, options[:fmt])
+      when :lines, :lineplots
+        @backend.lines(data, params, options[:fmt])
+      when :scatter, :s
+        @backend.scatter(data, params, options[:fmt])
+      when :density, :d
+        @backend.density(data, params, options[:fmt])
+      when :box, :boxplot
+        @backend.boxplot(data, params)
+      when :colors, :color, :colours, :colour
+        @backend.colors(options[:color_names])
+      else
+        raise "unrecognized plot_type: #{command}"
+      end
+    end
+
+    def output_data(input)
+      # Pass the input to subsequent pipelines
+      case options[:pass]
+      when IO
+        options[:pass].print(input)
+      else
+        if options[:pass]
+          File.open(options[:pass], 'w') do |f|
+            f.print(input)
           end
         end
+      end
+    end
 
-        case pass
-        when IO
-          pass.print(input)
-        else
-          if pass
-            File.open(pass, 'w') do |f|
-              f.print(input)
-            end
-          end
+    def output_plot(plot)
+      case options[:output]
+      when IO
+        plot.render(options[:output])
+      else
+        File.open(options[:output], 'w') do |f|
+          plot.render(f)
         end
       end
     end

lib/youplot/command/cmd_options.rb

@@ -0,0 +1,18 @@
+# frozen_string_literal: true
+
+module YouPlot
+  class Command
+    CmdOptions = Struct.new(
+      :delimiter,
+      :transpose,
+      :headers,
+      :pass,
+      :output,
+      :fmt,
+      :encoding,
+      :color_names,
+      :debug,
+      keyword_init: true
+    )
+  end
+end

lib/youplot/command/parser.rb

@@ -1,27 +1,30 @@
 # frozen_string_literal: true
 
 require 'optparse'
-require_relative 'params'
+require_relative 'cmd_options'
+require_relative 'plot_params'
 
 module YouPlot
   class Command
     class Parser
-      attr_reader :command, :params,
-                  :delimiter, :transpose, :headers, :pass, :output, :fmt,
-                  :color_names, :debug
+      attr_reader :command, :options, :params
 
       def initialize
-        @command     = nil
-        @params      = Params.new
+        @command = nil
 
-        @delimiter   = "\t"
-        @transpose   = false
-        @headers     = nil
-        @pass        = false
-        @output      = $stderr
-        @fmt         = 'xyy'
-        @debug       = false
-        @color_names = false
+        @options = CmdOptions.new(
+          delimiter: "\t",
+          transpose: false,
+          headers: nil,
+          pass: false,
+          output: $stderr,
+          fmt: 'xyy',
+          encoding: nil,
+          color_names: false,
+          debug: false
+        )
+
+        @params = PlotParams.new
       end
 
       def create_default_parser
@@ -32,21 +35,22 @@ module YouPlot
           opt.on_tail('') # Add a blank line at the end
           opt.separator('')
           opt.on('Common options:')
-          opt.on('-O', '--pass [VAL]', 'file to output standard input data to [stdout]',
+          opt.on('-O', '--pass [FILE]', 'file to output input data to [stdout]',
                  'for inserting YouPlot in the middle of Unix pipes') do |v|
-            @pass = v || $stdout
+            @options[:pass] = v || $stdout
           end
-          opt.on('-o', '--output VAL', 'file to output results to [stderr]') do |v|
-            @output = v
+          opt.on('-o', '--output [FILE]', 'file to output plots to [stdout]',
+                 'If no option is specified, plot will print to stderr') do |v|
+            @options[:output] = v || $stdout
           end
           opt.on('-d', '--delimiter VAL', String, 'use DELIM instead of TAB for field delimiter') do |v|
-            @delimiter = v
+            @options[:delimiter] = v
           end
           opt.on('-H', '--headers', TrueClass, 'specify that the input has header row') do |v|
-            @headers = v
+            @options[:headers] = v
           end
           opt.on('-T', '--transpose', TrueClass, 'transpose the axes of the input data') do |v|
-            @transpose = v
+            @options[:transpose] = v
           end
           opt.on('-t', '--title VAL', String, 'print string on the top of plot') do |v|
             params.title = v
@@ -78,8 +82,11 @@ module YouPlot
           opt.on('--[no-]labels', TrueClass, 'hide the labels') do |v|
             params.labels = v
           end
-          opt.on('--fmt VAL', String, 'xyxy : header is like x1, y1, x2, y2, x3, y3...', 'xyy  : header is like x, y1, y2, y2, y3...') do |v|
-            @fmt = v
+          opt.on('--progress', TrueClass, 'progressive') do |v|
+            @options[:progressive] = v
+          end
+          opt.on('--encoding VAL', String, 'Specify the input encoding') do |v|
+            @options[:encoding] = v
           end
           # Optparse adds the help option, but it doesn't show up in usage.
           # This is why you need the code below.
@@ -88,7 +95,7 @@ module YouPlot
             exit
           end
           opt.on('--debug', TrueClass, 'print preprocessed data') do |v|
-            @debug = v
+            @options[:debug] = v
           end
           yield opt if block_given?
         end
@@ -116,7 +123,7 @@ module YouPlot
                   scatter    s             draw a scatter plot
                   density    d             draw a density plot
                   boxplot    box           draw a horizontal boxplot
-                  colors                   show the list of available colors
+                  colors     color         show the list of available colors
 
                   count      c             draw a baplot based on the number of 
                                            occurrences (slow)
@@ -161,6 +168,9 @@ module YouPlot
             parser.on_head('--xscale VAL', String, 'axis scaling') do |v|
               params.xscale = v
             end
+            parser.on_head('--fmt VAL', String, 'xy : header is like x, y...', 'yx : header is like y, x...') do |v|
+              @options[:fmt] = v
+            end
 
           when :count, :c
             parser.on_head('--symbol VAL', String, 'character to be used to plot the bars') do |v|
@@ -188,6 +198,9 @@ module YouPlot
             parser.on_head('--ylim VAL', Array, 'plotting range for the y coordinate') do |v|
               params.ylim = v.take(2)
             end
+            parser.on_head('--fmt VAL', String, 'xy : header is like x, y...', 'yx : header is like y, x...') do |v|
+              @options[:fmt] = v
+            end
 
           when :lineplots, :lines
             parser.on_head('--canvas VAL', String) do |v|
@@ -199,6 +212,10 @@ module YouPlot
             parser.on_head('--ylim VAL', Array, 'plotting range for the y coordinate') do |v|
               params.ylim = v.take(2)
             end
+            parser.on_head('--fmt VAL', String, 'xyxy : header is like x1, y1, x2, y2, x3, y3...',
+                           'xyy  : header is like x, y1, y2, y2, y3...') do |v|
+              @options[:fmt] = v
+            end
 
           when :scatter, :s
             parser.on_head('--canvas VAL', String) do |v|
@@ -210,6 +227,10 @@ module YouPlot
             parser.on_head('--ylim VAL', Array, 'plotting range for the y coordinate') do |v|
               params.ylim = v.take(2)
             end
+            parser.on_head('--fmt VAL', String, 'xyxy : header is like x1, y1, x2, y2, x3, y3...',
+                           'xyy  : header is like x, y1, y2, y2, y3...') do |v|
+              @options[:fmt] = v
+            end
 
           when :density, :d
             parser.on_head('--grid', TrueClass) do |v|
@@ -221,15 +242,19 @@ module YouPlot
             parser.on_head('--ylim VAL', Array, 'plotting range for the y coordinate') do |v|
               params.ylim = v.take(2)
             end
+            parser.on('--fmt VAL', String, 'xyxy : header is like x1, y1, x2, y2, x3, y3...',
+                      'xyy  : header is like x, y1, y2, y2, y3...') do |v|
+              @options[:fmt] = v
+            end
 
           when :boxplot, :box
             parser.on_head('--xlim VAL', Array, 'plotting range for the x coordinate') do |v|
               params.xlim = v.take(2)
             end
 
-          when :colors
+          when :colors, :color, :colours, :colour
             parser.on_head('-n', '--names', 'show color names only', TrueClass) do |v|
-              @color_names = v
+              @options[:color_names] = v
             end
 
           else

lib/youplot/command/plot_params.rb

@@ -7,7 +7,7 @@ module YouPlot
     # * Here, I use Struct for 2 safety reason.
     # * The keys are static in Struct.
     # * Struct does not conflict with keyword arguments. Hash dose.
-    Params = Struct.new(
+    PlotParams = Struct.new(
       # Sort me!
       :title,
       :width,

lib/youplot/dsv_reader.rb

@@ -3,7 +3,8 @@
 require 'csv'
 
 module YouPlot
-  module Preprocessing
+  # Read and interpret Delimiter-separated values format file or stream.
+  module DSVReader
     module_function
 
     def input(input, delimiter, headers, transpose)
@@ -68,19 +69,5 @@ module YouPlot
         transpose2(arr)
       end
     end
-
-    def count_values(arr)
-      # tally was added in Ruby 2.7
-      if Enumerable.method_defined? :tally
-        arr.tally
-      else
-        # https://github.com/marcandre/backports
-        arr.each_with_object(Hash.new(0)) { |item, res| res[item] += 1 }
-           .tap { |h| h.default = nil }
-      end
-        .sort { |a, b| a[1] <=> b[1] }
-        .reverse
-        .transpose
-    end
   end
 end

lib/youplot/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module YouPlot
-  VERSION = '0.3.0'
+  VERSION = '0.3.2'
 end

test/fixtures/IRIStsv.tsv

@@ -0,0 +1,151 @@
+sepal_length	sepal_width	petal_length	petal_width	species
+5.1	3.5	1.4	0.2	Iris-setosa
+4.9	3	1.4	0.2	Iris-setosa
+4.7	3.2	1.3	0.2	Iris-setosa
+4.6	3.1	1.5	0.2	Iris-setosa
+5	3.6	1.4	0.2	Iris-setosa
+5.4	3.9	1.7	0.4	Iris-setosa
+4.6	3.4	1.4	0.3	Iris-setosa
+5	3.4	1.5	0.2	Iris-setosa
+4.4	2.9	1.4	0.2	Iris-setosa
+4.9	3.1	1.5	0.1	Iris-setosa
+5.4	3.7	1.5	0.2	Iris-setosa
+4.8	3.4	1.6	0.2	Iris-setosa
+4.8	3	1.4	0.1	Iris-setosa
+4.3	3	1.1	0.1	Iris-setosa
+5.8	4	1.2	0.2	Iris-setosa
+5.7	4.4	1.5	0.4	Iris-setosa
+5.4	3.9	1.3	0.4	Iris-setosa
+5.1	3.5	1.4	0.3	Iris-setosa
+5.7	3.8	1.7	0.3	Iris-setosa
+5.1	3.8	1.5	0.3	Iris-setosa
+5.4	3.4	1.7	0.2	Iris-setosa
+5.1	3.7	1.5	0.4	Iris-setosa
+4.6	3.6	1	0.2	Iris-setosa
+5.1	3.3	1.7	0.5	Iris-setosa
+4.8	3.4	1.9	0.2	Iris-setosa
+5	3	1.6	0.2	Iris-setosa
+5	3.4	1.6	0.4	Iris-setosa
+5.2	3.5	1.5	0.2	Iris-setosa
+5.2	3.4	1.4	0.2	Iris-setosa
+4.7	3.2	1.6	0.2	Iris-setosa
+4.8	3.1	1.6	0.2	Iris-setosa
+5.4	3.4	1.5	0.4	Iris-setosa
+5.2	4.1	1.5	0.1	Iris-setosa
+5.5	4.2	1.4	0.2	Iris-setosa
+4.9	3.1	1.5	0.1	Iris-setosa
+5	3.2	1.2	0.2	Iris-setosa
+5.5	3.5	1.3	0.2	Iris-setosa
+4.9	3.1	1.5	0.1	Iris-setosa
+4.4	3	1.3	0.2	Iris-setosa
+5.1	3.4	1.5	0.2	Iris-setosa
+5	3.5	1.3	0.3	Iris-setosa
+4.5	2.3	1.3	0.3	Iris-setosa
+4.4	3.2	1.3	0.2	Iris-setosa
+5	3.5	1.6	0.6	Iris-setosa
+5.1	3.8	1.9	0.4	Iris-setosa
+4.8	3	1.4	0.3	Iris-setosa
+5.1	3.8	1.6	0.2	Iris-setosa
+4.6	3.2	1.4	0.2	Iris-setosa
+5.3	3.7	1.5	0.2	Iris-setosa
+5	3.3	1.4	0.2	Iris-setosa
+7	3.2	4.7	1.4	Iris-versicolor
+6.4	3.2	4.5	1.5	Iris-versicolor
+6.9	3.1	4.9	1.5	Iris-versicolor
+5.5	2.3	4	1.3	Iris-versicolor
+6.5	2.8	4.6	1.5	Iris-versicolor
+5.7	2.8	4.5	1.3	Iris-versicolor
+6.3	3.3	4.7	1.6	Iris-versicolor
+4.9	2.4	3.3	1	Iris-versicolor
+6.6	2.9	4.6	1.3	Iris-versicolor
+5.2	2.7	3.9	1.4	Iris-versicolor
+5	2	3.5	1	Iris-versicolor
+5.9	3	4.2	1.5	Iris-versicolor
+6	2.2	4	1	Iris-versicolor
+6.1	2.9	4.7	1.4	Iris-versicolor
+5.6	2.9	3.6	1.3	Iris-versicolor
+6.7	3.1	4.4	1.4	Iris-versicolor
+5.6	3	4.5	1.5	Iris-versicolor
+5.8	2.7	4.1	1	Iris-versicolor
+6.2	2.2	4.5	1.5	Iris-versicolor
+5.6	2.5	3.9	1.1	Iris-versicolor
+5.9	3.2	4.8	1.8	Iris-versicolor
+6.1	2.8	4	1.3	Iris-versicolor
+6.3	2.5	4.9	1.5	Iris-versicolor
+6.1	2.8	4.7	1.2	Iris-versicolor
+6.4	2.9	4.3	1.3	Iris-versicolor
+6.6	3	4.4	1.4	Iris-versicolor
+6.8	2.8	4.8	1.4	Iris-versicolor
+6.7	3	5	1.7	Iris-versicolor
+6	2.9	4.5	1.5	Iris-versicolor
+5.7	2.6	3.5	1	Iris-versicolor
+5.5	2.4	3.8	1.1	Iris-versicolor
+5.5	2.4	3.7	1	Iris-versicolor
+5.8	2.7	3.9	1.2	Iris-versicolor
+6	2.7	5.1	1.6	Iris-versicolor
+5.4	3	4.5	1.5	Iris-versicolor
+6	3.4	4.5	1.6	Iris-versicolor
+6.7	3.1	4.7	1.5	Iris-versicolor
+6.3	2.3	4.4	1.3	Iris-versicolor
+5.6	3	4.1	1.3	Iris-versicolor
+5.5	2.5	4	1.3	Iris-versicolor
+5.5	2.6	4.4	1.2	Iris-versicolor
+6.1	3	4.6	1.4	Iris-versicolor
+5.8	2.6	4	1.2	Iris-versicolor
+5	2.3	3.3	1	Iris-versicolor
+5.6	2.7	4.2	1.3	Iris-versicolor
+5.7	3	4.2	1.2	Iris-versicolor
+5.7	2.9	4.2	1.3	Iris-versicolor
+6.2	2.9	4.3	1.3	Iris-versicolor
+5.1	2.5	3	1.1	Iris-versicolor
+5.7	2.8	4.1	1.3	Iris-versicolor
+6.3	3.3	6	2.5	Iris-virginica
+5.8	2.7	5.1	1.9	Iris-virginica
+7.1	3	5.9	2.1	Iris-virginica
+6.3	2.9	5.6	1.8	Iris-virginica
+6.5	3	5.8	2.2	Iris-virginica
+7.6	3	6.6	2.1	Iris-virginica
+4.9	2.5	4.5	1.7	Iris-virginica
+7.3	2.9	6.3	1.8	Iris-virginica
+6.7	2.5	5.8	1.8	Iris-virginica
+7.2	3.6	6.1	2.5	Iris-virginica
+6.5	3.2	5.1	2	Iris-virginica
+6.4	2.7	5.3	1.9	Iris-virginica
+6.8	3	5.5	2.1	Iris-virginica
+5.7	2.5	5	2	Iris-virginica
+5.8	2.8	5.1	2.4	Iris-virginica
+6.4	3.2	5.3	2.3	Iris-virginica
+6.5	3	5.5	1.8	Iris-virginica
+7.7	3.8	6.7	2.2	Iris-virginica
+7.7	2.6	6.9	2.3	Iris-virginica
+6	2.2	5	1.5	Iris-virginica
+6.9	3.2	5.7	2.3	Iris-virginica
+5.6	2.8	4.9	2	Iris-virginica
+7.7	2.8	6.7	2	Iris-virginica
+6.3	2.7	4.9	1.8	Iris-virginica
+6.7	3.3	5.7	2.1	Iris-virginica
+7.2	3.2	6	1.8	Iris-virginica
+6.2	2.8	4.8	1.8	Iris-virginica
+6.1	3	4.9	1.8	Iris-virginica
+6.4	2.8	5.6	2.1	Iris-virginica
+7.2	3	5.8	1.6	Iris-virginica
+7.4	2.8	6.1	1.9	Iris-virginica
+7.9	3.8	6.4	2	Iris-virginica
+6.4	2.8	5.6	2.2	Iris-virginica
+6.3	2.8	5.1	1.5	Iris-virginica
+6.1	2.6	5.6	1.4	Iris-virginica
+7.7	3	6.1	2.3	Iris-virginica
+6.3	3.4	5.6	2.4	Iris-virginica
+6.4	3.1	5.5	1.8	Iris-virginica
+6	3	4.8	1.8	Iris-virginica
+6.9	3.1	5.4	2.1	Iris-virginica
+6.7	3.1	5.6	2.4	Iris-virginica
+6.9	3.1	5.1	2.3	Iris-virginica
+5.8	2.7	5.1	1.9	Iris-virginica
+6.8	3.2	5.9	2.3	Iris-virginica
+6.7	3.3	5.7	2.5	Iris-virginica
+6.7	3	5.2	2.3	Iris-virginica
+6.3	2.5	5	1.9	Iris-virginica
+6.5	3	5.2	2	Iris-virginica
+6.2	3.4	5.4	2.3	Iris-virginica
+5.9	3	5.1	1.8	Iris-virginica

test/uplot/command_test.rb

@@ -1,102 +0,0 @@
-# frozen_string_literal: true
-
-require 'tempfile'
-require_relative '../test_helper'
-
-class YouPlotCommandTest < Test::Unit::TestCase
-  class << self
-    def startup
-      @stdin  = $stdin.dup
-      @stderr = $stderr.dup
-    end
-
-    def shutdown
-      $stdin  = @stdin
-      $stderr = @stderr
-    end
-  end
-
-  def setup
-    $stdin = File.open(File.expand_path('../fixtures/iris.csv', __dir__), 'r')
-    @tmp_file = Tempfile.new
-    $stderr = @tmp_file
-  end
-
-  def teardown
-    @tmp_file.close
-  end
-
-  def fixture(fname)
-    File.read(File.expand_path("../fixtures/#{fname}", __dir__))
-  end
-
-  test :bar do
-    YouPlot::Command.new(['bar', '-H', '-d,', '-t', 'IRIS-BARPLOT']).run
-    assert_equal fixture('iris-barplot.txt'), @tmp_file.read
-  end
-
-  test :barplot do
-    YouPlot::Command.new(['barplot', '-H', '-d,', '-t', 'IRIS-BARPLOT']).run
-    assert_equal fixture('iris-barplot.txt'), @tmp_file.read
-  end
-
-  test :hist do
-    YouPlot::Command.new(['hist', '-H', '-d,', '-t', 'IRIS-HISTOGRAM']).run
-    assert_equal fixture('iris-histogram.txt'), @tmp_file.read
-  end
-
-  test :histogram do
-    YouPlot::Command.new(['histogram', '-H', '-d,', '-t', 'IRIS-HISTOGRAM']).run
-    assert_equal fixture('iris-histogram.txt'), @tmp_file.read
-  end
-
-  test :line do
-    YouPlot::Command.new(['line', '-H', '-d,', '-t', 'IRIS-LINEPLOT']).run
-    assert_equal fixture('iris-lineplot.txt'), @tmp_file.read
-  end
-
-  test :lineplot do
-    YouPlot::Command.new(['lineplot', '-H', '-d,', '-t', 'IRIS-LINEPLOT']).run
-    assert_equal fixture('iris-lineplot.txt'), @tmp_file.read
-  end
-
-  test :lines do
-    YouPlot::Command.new(['lines', '-H', '-d,', '-t', 'IRIS-LINEPLOTS']).run
-    assert_equal fixture('iris-lineplots.txt'), @tmp_file.read
-  end
-
-  test :lineplots do
-    YouPlot::Command.new(['lineplots', '-H', '-d,', '-t', 'IRIS-LINEPLOTS']).run
-    assert_equal fixture('iris-lineplots.txt'), @tmp_file.read
-  end
-
-  test :s do
-    YouPlot::Command.new(['s', '-H', '-d,', '-t', 'IRIS-SCATTER']).run
-    assert_equal fixture('iris-scatter.txt'), @tmp_file.read
-  end
-
-  test :scatter do
-    YouPlot::Command.new(['scatter', '-H', '-d,', '-t', 'IRIS-SCATTER']).run
-    assert_equal fixture('iris-scatter.txt'), @tmp_file.read
-  end
-
-  test :d do
-    YouPlot::Command.new(['d', '-H', '-d,', '-t', 'IRIS-DENSITY']).run
-    assert_equal fixture('iris-density.txt'), @tmp_file.read
-  end
-
-  test :density do
-    YouPlot::Command.new(['density', '-H', '-d,', '-t', 'IRIS-DENSITY']).run
-    assert_equal fixture('iris-density.txt'), @tmp_file.read
-  end
-
-  test :box do
-    YouPlot::Command.new(['box', '-H', '-d,', '-t', 'IRIS-BOXPLOT']).run
-    assert_equal fixture('iris-boxplot.txt'), @tmp_file.read
-  end
-
-  test :boxplot do
-    YouPlot::Command.new(['boxplot', '-H', '-d,', '-t', 'IRIS-BOXPLOT']).run
-    assert_equal fixture('iris-boxplot.txt'), @tmp_file.read
-  end
-end

test/youplot/backends/processing_test.rb

@@ -0,0 +1,11 @@
+# frozen_string_literal: true
+
+require_relative '../../test_helper'
+
+class YouPlotCommandTest < Test::Unit::TestCase
+  test :count_values do
+    @m = YouPlot::Backends::Processing
+    assert_equal([%i[a b c], [3, 2, 1]], @m.count_values(%i[a a a b b c]))
+    assert_equal([%i[c b a], [3, 2, 1]], @m.count_values(%i[a b b c c c]))
+  end
+end

test/youplot/backends/unicode_plot_backend_test.rb

@@ -1,6 +1,6 @@
 # frozen_string_literal: true
 
-require_relative '../test_helper'
+require_relative '../../test_helper'
 
 class YouPlotPlotTest < Test::Unit::TestCase
 end

test/youplot/command_test.rb

@@ -0,0 +1,131 @@
+# frozen_string_literal: true
+
+require 'tempfile'
+require_relative '../test_helper'
+
+class YouPlotCommandTest < Test::Unit::TestCase
+  class << self
+    def startup
+      @stdin  = $stdin.dup
+      @stdout = $stdout.dup
+      @stderr = $stderr.dup
+    end
+
+    def shutdown
+      $stdin  = @stdin
+      $stdout = @stdout
+      $stderr = @stderr
+    end
+  end
+
+  def setup
+    $stdin = File.open(File.expand_path('../fixtures/iris.csv', __dir__), 'r')
+    @stderr_file = Tempfile.new
+    @stdout_file = Tempfile.new
+    $stderr = @stderr_file
+    $stdout = @stdout_file
+  end
+
+  def teardown
+    @stderr_file.close
+  end
+
+  def fixture(fname)
+    File.read(File.expand_path("../fixtures/#{fname}", __dir__))
+  end
+
+  test :bar do
+    YouPlot::Command.new(['bar', '-H', '-d,', '-t', 'IRIS-BARPLOT']).run
+    assert_equal fixture('iris-barplot.txt'), @stderr_file.read
+  end
+
+  test :barplot do
+    YouPlot::Command.new(['barplot', '-H', '-d,', '-t', 'IRIS-BARPLOT']).run
+    assert_equal fixture('iris-barplot.txt'), @stderr_file.read
+  end
+
+  test :hist do
+    YouPlot::Command.new(['hist', '-H', '-d,', '-t', 'IRIS-HISTOGRAM']).run
+    assert_equal fixture('iris-histogram.txt'), @stderr_file.read
+  end
+
+  test :histogram do
+    YouPlot::Command.new(['histogram', '-H', '-d,', '-t', 'IRIS-HISTOGRAM']).run
+    assert_equal fixture('iris-histogram.txt'), @stderr_file.read
+  end
+
+  test :line do
+    YouPlot::Command.new(['line', '-H', '-d,', '-t', 'IRIS-LINEPLOT']).run
+    assert_equal fixture('iris-lineplot.txt'), @stderr_file.read
+  end
+
+  test :lineplot do
+    YouPlot::Command.new(['lineplot', '-H', '-d,', '-t', 'IRIS-LINEPLOT']).run
+    assert_equal fixture('iris-lineplot.txt'), @stderr_file.read
+  end
+
+  test :lines do
+    YouPlot::Command.new(['lines', '-H', '-d,', '-t', 'IRIS-LINEPLOTS']).run
+    assert_equal fixture('iris-lineplots.txt'), @stderr_file.read
+  end
+
+  test :lineplots do
+    YouPlot::Command.new(['lineplots', '-H', '-d,', '-t', 'IRIS-LINEPLOTS']).run
+    assert_equal fixture('iris-lineplots.txt'), @stderr_file.read
+  end
+
+  test :s do
+    YouPlot::Command.new(['s', '-H', '-d,', '-t', 'IRIS-SCATTER']).run
+    assert_equal fixture('iris-scatter.txt'), @stderr_file.read
+  end
+
+  test :scatter do
+    YouPlot::Command.new(['scatter', '-H', '-d,', '-t', 'IRIS-SCATTER']).run
+    assert_equal fixture('iris-scatter.txt'), @stderr_file.read
+  end
+
+  test :d do
+    YouPlot::Command.new(['d', '-H', '-d,', '-t', 'IRIS-DENSITY']).run
+    assert_equal fixture('iris-density.txt'), @stderr_file.read
+  end
+
+  test :density do
+    YouPlot::Command.new(['density', '-H', '-d,', '-t', 'IRIS-DENSITY']).run
+    assert_equal fixture('iris-density.txt'), @stderr_file.read
+  end
+
+  test :box do
+    YouPlot::Command.new(['box', '-H', '-d,', '-t', 'IRIS-BOXPLOT']).run
+    assert_equal fixture('iris-boxplot.txt'), @stderr_file.read
+  end
+
+  test :boxplot do
+    YouPlot::Command.new(['boxplot', '-H', '-d,', '-t', 'IRIS-BOXPLOT']).run
+    assert_equal fixture('iris-boxplot.txt'), @stderr_file.read
+  end
+
+  test :plot_output_stdout do
+    YouPlot::Command.new(['bar', '-o', '-H', '-d,', '-t', 'IRIS-BARPLOT']).run
+    assert_equal '', @stderr_file.read
+  end
+
+  test :data_output_stdout do
+    YouPlot::Command.new(['bar', '-O', '-H', '-d,', '-t', 'IRIS-BARPLOT']).run
+    assert_equal fixture('iris-barplot.txt'), @stderr_file.read
+    assert_equal File.read(File.expand_path('../fixtures/iris.csv', __dir__)), @stdout_file.read
+  end
+
+  %i[colors color colours colour].each do |cmd_name|
+    test cmd_name do
+      YouPlot::Command.new([cmd_name.to_s]).run
+      assert_equal fixture('colors.txt'), @stderr_file.read
+      assert_equal '', @stdout_file.read
+    end
+  end
+
+  test :colors_output_stdout do
+    YouPlot::Command.new(['colors', '-o']).run
+    assert_equal '', @stderr_file.read
+    assert_equal fixture('colors.txt'), @stdout_file.read
+  end
+end

test/youplot/dev_reader_test.rb

@@ -2,9 +2,9 @@
 
 require_relative '../test_helper'
 
-class YouPlotPreprocessingTest < Test::Unit::TestCase
+class YouPlotDSVReaderTest < Test::Unit::TestCase
   def setup
-    @m = YouPlot::Preprocessing
+    @m = YouPlot::DSVReader
   end
 
   test :transpose2 do
@@ -124,9 +124,4 @@ class YouPlotPreprocessingTest < Test::Unit::TestCase
                                              [2, 4],
                                              [3, 5, 6]], false, false))
   end
-
-  test :count_values do
-    assert_equal([%i[a b c], [3, 2, 1]], @m.count_values(%i[a a a b b c]))
-    assert_equal([%i[c b a], [3, 2, 1]], @m.count_values(%i[a b b c c c]))
-  end
 end

test/youplot_test.rb

@@ -1,6 +1,6 @@
 # frozen_string_literal: true
 
-require 'test_helper'
+require_relative 'test_helper'
 
 class YouPlotTest < Test::Unit::TestCase
   def test_that_it_has_a_version_number