youplot 0.3.3 → 0.4.2

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data/README.md

@@ -1,16 +1,19 @@
-<p align="center">
-  <img src="https://user-images.githubusercontent.com/5798442/103439598-9e952a00-4c81-11eb-881f-67c593bb7861.png" width="75%" height="75%" />
-</p>
-
-![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)
-
-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)
+<div align="center">
+  <img src="logo.svg" width="66%" height="66%" />
+  
+  <hr>
+  
+  ![Build Status](https://github.com/red-data-tools/YouPlot/workflows/test/badge.svg)
+  [![Gem Version](https://badge.fury.io/rb/youplot.svg)](https://badge.fury.io/rb/youplot)
+  [![Docs Stable](https://img.shields.io/badge/docs-stable-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)
+  
+  YouPlot is a command line tool that draws plots in a terminal.
+
+  :bar_chart: Powered by [UnicodePlot](https://github.com/red-data-tools/unicode_plot.rb)
+  
+</div>
 
 ## Installation
 
@@ -106,8 +109,8 @@ In this example, YouPlot counts the number of chromosomes where the gene is loca
 
 ```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
+| grep -v '#' | grep 'gene' | cut -f1 \
+| uplot count -t "The number of human gene annotations per chromosome"  -c blue
 ```
 
 <p align="center">
@@ -119,7 +122,7 @@ This is fine in most cases, as long as the data size is small. If you want to vi
 
 ```sh
 cat gencode.v35.annotation.gff3 | grep -v '#' | grep 'gene' | cut -f1 \
-|sort | uniq -c | sort -nrk2 | awk '{print $2,$1}' \
+| sort | uniq -c | sort -nrk2 | awk '{print $2,$1}' \
 | uplot bar -d ' ' -t "The number of human gene annotations per chromosome"  -c blue
 ```
 
@@ -130,15 +133,15 @@ cat gencode.v35.annotation.gff3 | grep -v '#' | grep 'gene' | cut -f1 \
 Wouldn't it be a 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.
 
-### how to use YouPlot?
+### How to use YouPlot?
 
 `uplot` is the shortened form of `youplot`. You can use either.
 
-|                                   |                                                |
-|-----------------------------------|------------------------------------------------|
-| 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` |
+| Command                                        | Description                       |
+|------------------------------------------------|-----------------------------------|
+| `cat data.tsv \| uplot <command> [options]`    | Take input from stdin             |
+| `uplot <command> [options] data.tsv ...`       | Take input from files             |
+| `pipeline1 \| uplot <command> -O \| pipeline2` | Outputs data from stdin to stdout |
 
 ### Where to output the plot?
 
@@ -148,7 +151,8 @@ 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 shown 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.
+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?
 
@@ -176,11 +180,21 @@ If your input data contains a header line, you need to specify the `-H` option.
 
 ### How to specify the delimiter?
 
-Use the `-d` option. To specify a blank space, you can use `uplot bar -d ' ' data.txt`. You do not need to use `-d` option for tab-delimited text since the default value is tab.
+Use the `-d` option. To specify a blank space, you can use `uplot bar -d ' ' data.txt`. 
+You do not need to use `-d` option for tab-delimited text since the default value is tab.
 
 ### Is there a way to specify a column as the x-axis or y-axis?
 
-Not yet. In principle, YouPlot treats the first column as the X axis and the second column as the Y axis. When working with multiple series, the first row is the X axis, the second row is series 1, the third row is series 2, and so on. If you pass only one column of data for `line` and `bar`, YouPlot will automatically use a sequential number starting from 1 as the X-axis. The　`--fmt xyy`, `--fmt xyxy` and `--fmt yx` options give you a few more choices. See `youplot <command> --help` for more details. YouPlot has limited functionalities, but you can use shell scripts such as `awk '{print $2, $1}'` to swap lines.
+Not yet. 
+YouPlot treats the first column as the X axis and the second column as the Y axis. 
+When working with multiple series, the first column is the X axis, the second column is series Y1, the third column is series Y2, and so on. 
+If you pass only one column of data for `line` and `bar`, YouPlot will automatically use a sequential number starting from 1 as the X-axis. 
+
+* `--fmt xyy` `--fmt xyxy` `--fmt yx` options give you a few more choices. 
+See `youplot <command> --help` for more details. 
+
+* Use `awk '{print $2, $1}'` to swap lines.
+* Use `paste` to concatenate series.
 
 ### How to plot real-time data?
 
@@ -201,7 +215,7 @@ Usage: uplot histogram [options] <in.tsv>
 
 Options for histogram:
         --symbol VAL         character to be used to plot the bars
-        --closed VAL
+        --closed VAL         side of the intervals to be closed [left]
     -n, --nbins VAL          approximate number of bins
 
 Options:
@@ -216,23 +230,31 @@ uplot colors
 
 ## Contributing
 
-* [Report bugs](https://github.com/kojix2/youplot/issues)
-* Fix bugs and [submit pull requests](https://github.com/kojix2/youplot/pulls)
+YouPlot is a library under development, so even small improvements like typofix are welcome!
+Please feel free to send us your pull requests.
+
+* [Report bugs](https://github.com/red-data-tools/YouPlot/issues)
+* Fix bugs and [submit pull requests](https://github.com/red-data-tools/YouPlot/pulls)
 * Write, clarify, or fix documentation
   * English corrections by native speakers are welcome.
 * Suggest or add new features
-
+* Make a donation
 
 ### Development
 
 ```sh
-git clone https://github.com/your_name/GR.rb # Clone the Git repo
-cd GR.rb
+# fork the main repository by clicking the Fork button. 
+git clone https://github.com/your_name/YouPlot
 bundle install             # Install the gem dependencies
 bundle exec rake test      # Run the test
 bundle exec rake install   # Installation from source code
 ```
 
+### Acknowledgements
+
+* [sampo grafiikka](https://jypg.net/sampo_grafiikka) - Project logo creation
+* [yutaas](https://github.com/yutaas) - English proofreading
+
 ## License
 
 [MIT License](https://opensource.org/licenses/MIT).

data/exe/uplot

@@ -3,4 +3,4 @@
 
 require 'youplot'
 
-YouPlot::Command.new.run
+YouPlot::Command.new.run_as_executable

data/exe/youplot

@@ -3,4 +3,4 @@
 
 require 'youplot'
 
-YouPlot::Command.new.run
+YouPlot::Command.new.run_as_executable

data/lib/youplot.rb

@@ -1,9 +1,17 @@
 # frozen_string_literal: true
 
-require 'unicode_plot'
-require 'youplot/version'
-require 'youplot/dsv'
-require 'youplot/command'
+require_relative 'youplot/version'
+require_relative 'youplot/dsv'
+require_relative 'youplot/parameters'
+require_relative 'youplot/command'
 
 module YouPlot
+  class << self
+    attr_accessor :run_as_executable
+
+    def run_as_executable?
+      @run_as_executable
+    end
+  end
+  @run_as_executable = false
 end

data/lib/youplot/backends/processing.rb

@@ -6,18 +6,30 @@ module YouPlot
     module Processing
       module_function
 
-      def count_values(arr)
+      def count_values(arr, tally: true, reverse: false)
         # 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 }
+        result = \
+          if tally && Enumerable.method_defined?(:tally)
+            arr.tally
+          else
+            # value_counts Enumerable::Statistics
+            arr.value_counts(dropna: false)
+          end
+
+        # sorting
+        result = result.sort do |a, b|
+          # compare values
+          r = b[1] <=> a[1]
+          # If the values are the same, compare by name
+          r = a[0] <=> b[0] if r.zero?
+          r
         end
-          .sort { |a, b| a[1] <=> b[1] }
-          .reverse
-          .transpose
+
+        # --reverse option
+        result.reverse! if reverse
+
+        # prepare for barplot
+        result.transpose
       end
     end
   end

data/lib/youplot/backends/{unicode_plot_backend.rb → unicode_plot.rb}

@@ -1,20 +1,25 @@
 # frozen_string_literal: true
 
+# UnicodePlot - Plot your data by Unicode characters
+# https://github.com/red-data-tools/unicode_plot.rb
+
 require_relative 'processing'
 require 'unicode_plot'
 
 module YouPlot
   # plotting functions.
   module Backends
-    module UnicodePlotBackend
+    module UnicodePlot
+      class Error < StandardError; end
+
       module_function
 
-      def barplot(data, params, fmt = nil, count: false)
+      def barplot(data, params, fmt = nil, count: false, reverse: false)
         headers = data.headers
         series = data.series
         # `uplot count`
         if count
-          series = Processing.count_values(series[0])
+          series = Processing.count_values(series[0], reverse: reverse)
           params.title = headers[0] if headers
         end
         if series.size == 1
@@ -37,7 +42,7 @@ module YouPlot
           labels = series[x_col]
           values = series[y_col].map(&:to_f)
         end
-        UnicodePlot.barplot(labels, values, **params.to_hc)
+        ::UnicodePlot.barplot(labels, values, **params.to_hc)
       end
 
       def histogram(data, params)
@@ -45,7 +50,7 @@ module YouPlot
         series = data.series
         params.title ||= data.headers[0] if headers
         values = series[0].map(&:to_f)
-        UnicodePlot.histogram(values, **params.to_hc)
+        ::UnicodePlot.histogram(values, **params.to_hc)
       end
 
       def line(data, params, fmt = nil)
@@ -55,7 +60,7 @@ module YouPlot
           # If there is only one series, it is assumed to be sequential data.
           params.ylabel ||= headers[0] if headers
           y = series[0].map(&:to_f)
-          UnicodePlot.lineplot(y, **params.to_hc)
+          ::UnicodePlot.lineplot(y, **params.to_hc)
         else
           # If there are 2 or more series...
           if fmt == 'yx'
@@ -73,7 +78,7 @@ module YouPlot
           end
           x = series[x_col].map(&:to_f)
           y = series[y_col].map(&:to_f)
-          UnicodePlot.lineplot(x, y, **params.to_hc)
+          ::UnicodePlot.lineplot(x, y, **params.to_hc)
         end
       end
 
@@ -90,10 +95,11 @@ module YouPlot
           params.name   ||= headers[1]
           params.xlabel ||= headers[0]
         end
+        params.xlim ||= series[0].flatten.minmax # why need?
         params.ylim ||= series[1..-1].flatten.minmax # why need?
-        plot = UnicodePlot.public_send(method1, series[0], series[1], **params.to_hc)
+        plot = ::UnicodePlot.public_send(method1, series[0], series[1], **params.to_hc)
         2.upto(series.size - 1) do |i|
-          UnicodePlot.public_send(method2, plot, series[0], series[i], name: headers&.[](i))
+          ::UnicodePlot.public_send(method2, plot, series[0], series[i], name: headers&.[](i))
         end
         plot
       end
@@ -103,14 +109,15 @@ module YouPlot
         series = data.series
         method2 = get_method2(method1)
         series.map! { |s| s.map(&:to_f) }
-        series = series.each_slice(2).to_a
+        series2 = series.each_slice(2).to_a
+        series = nil
         params.name ||= headers[0] if headers
-        params.xlim = series.map(&:first).flatten.minmax # why need?
-        params.ylim = series.map(&:last).flatten.minmax  # why need?
-        x1, y1 = series.shift
-        plot = UnicodePlot.public_send(method1, x1, y1, **params.to_hc)
-        series.each_with_index do |(xi, yi), i|
-          UnicodePlot.public_send(method2, plot, xi, yi, name: headers&.[]((i + 1) * 2))
+        params.xlim ||= series2.map(&:first).flatten.minmax # why need?
+        params.ylim ||= series2.map(&:last).flatten.minmax # why need?
+        x1, y1 = series2.shift
+        plot = ::UnicodePlot.public_send(method1, x1, y1, **params.to_hc)
+        series2.each_with_index do |(xi, yi), i|
+          ::UnicodePlot.public_send(method2, plot, xi, yi, name: headers&.[]((i + 1) * 2))
         end
         plot
       end
@@ -148,13 +155,13 @@ module YouPlot
         series = data.series
         headers ||= (1..series.size).map(&:to_s)
         series.map! { |s| s.map(&:to_f) }
-        UnicodePlot.boxplot(headers, series, **params.to_hc)
+        ::UnicodePlot.boxplot(headers, series, **params.to_hc)
       end
 
       def colors(color_names = false)
         # FIXME
         s = String.new
-        UnicodePlot::StyledPrinter::TEXT_COLORS.each do |k, v|
+        ::UnicodePlot::StyledPrinter::TEXT_COLORS.each do |k, v|
           s << v
           s << k.to_s
           unless color_names
@@ -174,19 +181,25 @@ module YouPlot
       def check_series_size(data, fmt)
         series = data.series
         if series.size == 1
-          warn 'youplot: There is only one series of input data. Please check the delimiter.'
-          warn ''
-          warn "  Headers: \e[35m#{data.headers.inspect}\e[0m"
-          warn "  The first item is: \e[35m\"#{series[0][0]}\"\e[0m"
-          warn "  The last item is : \e[35m\"#{series[0][-1]}\"\e[0m"
-          exit 1
+          warn <<~EOS
+            youplot: There is only one series of input data. Please check the delimiter.
+
+            Headers: \e[35m#{data.headers.inspect}\e[0m
+            The first item is: \e[35m\"#{series[0][0]}\"\e[0m
+            The last item is : \e[35m\"#{series[0][-1]}\"\e[0m
+          EOS
+          # NOTE: Error messages cannot be colored.
+          YouPlot.run_as_executable ? exit(1) : raise(Error)
         end
         if fmt == 'xyxy' && series.size.odd?
-          warn 'YouPlot: In the xyxy format, the number of series must be even.'
-          warn ''
-          warn "  Number of series: \e[35m#{series.size}\e[0m"
-          warn "  Headers: \e[35m#{data.headers.inspect}\e[0m"
-          exit 1
+          warn <<~EOS
+            YouPlot: In the xyxy format, the number of series must be even.
+
+            Number of series: \e[35m#{series.size}\e[0m
+            Headers: \e[35m#{data.headers.inspect}\e[0m
+          EOS
+          # NOTE: Error messages cannot be colored.
+          YouPlot.run_as_executable ? exit(1) : raise(Error)
         end
       end
     end

data/lib/youplot/command.rb

@@ -1,10 +1,10 @@
 # frozen_string_literal: true
 
 require_relative 'dsv'
-require_relative 'command/parser'
+require_relative 'parser'
 
 # FIXME
-require_relative 'backends/unicode_plot_backend'
+require_relative 'backends/unicode_plot'
 
 module YouPlot
   Data = Struct.new(:headers, :series)
@@ -19,7 +19,12 @@ module YouPlot
       @command = nil
       @params  = nil
       @options = nil
-      @backend = YouPlot::Backends::UnicodePlotBackend
+      @backend = YouPlot::Backends::UnicodePlot
+    end
+
+    def run_as_executable
+      YouPlot.run_as_executable = true
+      run
     end
 
     def run
@@ -28,17 +33,34 @@ module YouPlot
       @options ||= parser.options
       @params  ||= parser.params
 
+      # color command
       if %i[colors color colours colour].include? @command
         plot = create_plot
         output_plot(plot)
-      elsif options[:progressive]
+        return
+      end
+
+      # progressive mode
+      if options[:progressive]
         stop = false
         Signal.trap(:INT) { stop = true }
+
+        # make cursor invisible
+        options[:output].print "\e[?25l"
+
+        # mainloop
         while (input = Kernel.gets)
-          main_progressive(input)
+          n = main_progressive(input)
           break if stop
+
+          options[:output].print "\e[#{n}F"
         end
+
         options[:output].print "\e[0J"
+        # make cursor visible
+        options[:output].print "\e[?25h"
+
+      # normal mode
       else
         # Sometimes the input file does not end with a newline code.
         while (input = Kernel.gets(nil))
@@ -50,13 +72,32 @@ module YouPlot
     private
 
     def main(input)
+      # Outputs input data to a file or stdout.
       output_data(input)
 
-      @data = read_dsv(input)
+      @data = parse_dsv(input)
 
+      # Debug mode, show parsed results
       pp @data if options[:debug]
 
-      plot = create_plot
+      # When run as a program instead of a library
+      if YouPlot.run_as_executable?
+        begin
+          plot = create_plot
+        rescue ArgumentError => e
+          # Show only one line of error.
+          warn e.backtrace[0]
+          # Show error message in purple
+          warn "\e[35m#{e}\e[0m"
+          # Explicitly terminated with exit code: 1
+          exit 1
+        end
+
+      # When running YouPlot as a library (e.g. for testing)
+      else
+        plot = create_plot
+      end
+
       output_plot(plot)
     end
 
@@ -76,15 +117,28 @@ module YouPlot
       @raw_data << input
 
       # FIXME
-      @data = read_dsv(@raw_data)
+      @data = parse_dsv(@raw_data)
 
       plot = create_plot
       output_plot_progressive(plot)
     end
 
-    def read_dsv(input)
-      input = input.dup.force_encoding(options[:encoding]).encode('utf-8') if options[:encoding]
-      DSV.parse(input, options[:delimiter], options[:headers], options[:transpose])
+    def parse_dsv(input)
+      # If encoding is specified, convert to UTF-8
+      if options[:encoding]
+        input.force_encoding(options[:encoding])
+             .encode!('utf-8')
+      end
+
+      begin
+        data = DSV.parse(input, options[:delimiter], options[:headers], options[:transpose])
+      rescue CSV::MalformedCSVError => e
+        warn 'Failed to parse the text. '
+        warn 'Please try to set the correct character encoding with --encoding option.'
+        raise e
+      end
+
+      data
     end
 
     def create_plot
@@ -92,7 +146,7 @@ module YouPlot
       when :bar, :barplot
         @backend.barplot(data, params, options[:fmt])
       when :count, :c
-        @backend.barplot(data, params, count: true)
+        @backend.barplot(data, params, count: true, reverse: options[:reverse])
       when :hist, :histogram
         @backend.histogram(data, params)
       when :line, :lineplot
@@ -128,9 +182,9 @@ module YouPlot
 
     def output_plot(plot)
       case options[:output]
-      when IO
+      when IO, StringIO
         plot.render(options[:output])
-      else
+      when String, Tempfile
         File.open(options[:output], 'w') do |f|
           plot.render(f)
         end
@@ -139,7 +193,7 @@ module YouPlot
 
     def output_plot_progressive(plot)
       case options[:output]
-      when IO
+      when IO, StringIO
         # RefactorMe
         out = StringIO.new(String.new)
         def out.tty?
@@ -154,8 +208,7 @@ module YouPlot
         end
         options[:output].print "\e[0J"
         options[:output].flush
-        n = out.string.lines.size
-        options[:output].print "\e[#{n}F"
+        out.string.lines.size
       else
         raise 'In progressive mode, output to a file is not possible.'
       end