youplot 0.3.4 → 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?
 
@@ -216,18 +230,21 @@ 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
@@ -235,7 +252,6 @@ bundle exec rake install   # Installation from source code
 
 ### Acknowledgements
 
-* [Red Data Tools](https://github.com/red-data-tools) - Technical support
 * [sampo grafiikka](https://jypg.net/sampo_grafiikka) - Project logo creation
 * [yutaas](https://github.com/yutaas) - English proofreading
 

data/lib/youplot/backends/processing.rb

@@ -6,18 +6,30 @@ module YouPlot
     module Processing
       module_function
 
-      def count_values(arr, tally: true)
+      def count_values(arr, tally: true, reverse: false)
         # tally was added in Ruby 2.7
-        if tally && 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}

@@ -1,22 +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
@@ -39,19 +42,7 @@ module YouPlot
           labels = series[x_col]
           values = series[y_col].map(&:to_f)
         end
-        begin
-          UnicodePlot.barplot(labels, values, **params.to_hc)
-        # UnicodePlot error:
-        # All values have to be positive. Negative bars are not supported.
-        rescue ArgumentError => e
-          if YouPlot.run_as_executable?
-            warn e.backtrace[0]
-            warn "\e[35m#{e}\e[0m"
-            exit 1
-          else
-            raise e
-          end
-        end
+        ::UnicodePlot.barplot(labels, values, **params.to_hc)
       end
 
       def histogram(data, params)
@@ -59,7 +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)
@@ -69,7 +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'
@@ -87,7 +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
 
@@ -106,9 +97,9 @@ module YouPlot
         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
@@ -124,9 +115,9 @@ module YouPlot
         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)
+        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))
+          ::UnicodePlot.public_send(method2, plot, xi, yi, name: headers&.[]((i + 1) * 2))
         end
         plot
       end
@@ -164,13 +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
@@ -190,18 +181,24 @@ 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"
+          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"
+          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

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 +19,7 @@ module YouPlot
       @command = nil
       @params  = nil
       @options = nil
-      @backend = YouPlot::Backends::UnicodePlotBackend
+      @backend = YouPlot::Backends::UnicodePlot
     end
 
     def run_as_executable
@@ -33,21 +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 }
-        options[:output].print "\e[?25l" # make cursor invisible
+
+        # make cursor invisible
+        options[:output].print "\e[?25l"
+
+        # mainloop
         while (input = Kernel.gets)
           n = main_progressive(input)
           break if stop
 
           options[:output].print "\e[#{n}F"
         end
+
         options[:output].print "\e[0J"
-        options[:output].print "\e[?25h" # make cursor visible
+        # 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))
@@ -59,13 +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
 
@@ -85,15 +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
@@ -101,7 +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
@@ -137,9 +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
@@ -148,7 +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?

data/lib/youplot/dsv.rb

@@ -3,41 +3,49 @@
 require 'csv'
 
 module YouPlot
-  # Read and interpret Delimiter-separated values format file or stream.
+  # Module to handle DSV (Delimiter-separated values) format.
+  # Extract header and series.
   module DSV
     module_function
 
     def parse(input, delimiter, headers, transpose)
-      arr = parse_as_csv(input, delimiter)
+      # Parse as CSV
+      arr = CSV.parse(input, col_sep: delimiter)
+
+      # Remove blank lines
+      arr.delete_if do |i|
+        i == [] or i.all?(&:nil?)
+      end
+
+      # get header
       headers = get_headers(arr, headers, transpose)
+
+      # get series
       series = get_series(arr, headers, transpose)
-      if headers.nil?
-        Data.new(headers, series)
-      else
-        if headers.include?(nil)
-          warn "\e[35mHeaders contains nil in it.\e[0m"
-        elsif headers.include? ''
-          warn "\e[35mHeaders contains \"\" in it.\e[0m"
-        end
-        h_size = headers.size
-        s_size = series.size
-        if h_size == s_size
-          Data.new(headers, series)
-        elsif h_size > s_size
-          warn "\e[35mThe number of headers is greater than the number of series.\e[0m"
-          exit 1 if YouPlot.run_as_executable?
-        elsif h_size < s_size
-          warn "\e[35mThe number of headers is less than the number of series.\e[0m"
-          exit 1 if YouPlot.run_as_executable?
-        end
+
+      # Return if No header
+      return Data.new(headers, series) if headers.nil?
+
+      # Warn if header contains nil
+      warn "\e[35mHeaders contains nil in it.\e[0m" if headers.include?(nil)
+
+      # Warn if header contains ''
+      warn "\e[35mHeaders contains \"\" in it.\e[0m" if headers.include? ''
+
+      # Make sure the number of elements in the header matches the number of series.
+      h_size = headers.size
+      s_size = series.size
+
+      if h_size > s_size
+        warn "\e[35mThe number of headers is greater than the number of series.\e[0m"
+        exit 1 if YouPlot.run_as_executable?
+
+      elsif h_size < s_size
+        warn "\e[35mThe number of headers is less than the number of series.\e[0m"
+        exit 1 if YouPlot.run_as_executable?
       end
-    end
 
-    def parse_as_csv(input, delimiter)
-      CSV.parse(input, col_sep: delimiter)
-         .delete_if do |i|
-           i == [] or i.all? nil
-         end
+      Data.new(headers, series) if h_size == s_size
     end
 
     # Transpose different sized ruby arrays
@@ -47,31 +55,33 @@ module YouPlot
     end
 
     def get_headers(arr, headers, transpose)
-      if headers
-        if transpose
-          arr.map(&:first)
-        else
-          arr[0]
-        end
-      end
+      # header(-)
+      return nil unless headers
+
+      # header(+) trenspose(+)
+      return arr.map(&:first) if transpose
+
+      # header(+) transpose(-)
+      arr[0]
     end
 
     def get_series(arr, headers, transpose)
-      if headers
-        if arr.size > 1
-          if transpose
-            arr.map { |row| row[1..-1] }
-          else
-            transpose2(arr[1..-1])
-          end
-        else
-          Array.new(arr[0].size, [])
-        end
-      elsif transpose
-        arr
-      else
-        transpose2(arr)
+      # header(-)
+      unless headers
+        return arr if transpose
+
+        return transpose2(arr)
       end
+
+      # header(+) but no element in the series.
+      # TODO: should raise error?
+      return Array.new(arr[0].size, []) if arr.size == 1
+
+      # header(+) transpose(+)
+      return arr.map { |row| row[1..-1] } if transpose
+
+      # header(+) transpose(-)
+      transpose2(arr[1..-1])
     end
   end
 end

data/lib/youplot/options.rb

@@ -0,0 +1,18 @@
+# frozen_string_literal: true
+
+module YouPlot
+  # Command line options that are not Plot parameters
+  Options = Struct.new(
+    :delimiter,
+    :transpose,
+    :headers,
+    :pass,
+    :output,
+    :fmt,
+    :progressive,
+    :encoding,
+    :reverse,      # count
+    :color_names,  # color
+    :debug
+  )
+end