youplot 0.3.5 → 0.4.3

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

@@ -1,16 +1,16 @@
-<p align="center">
-  <img src="logo.svg" width="60%" height="60%" />
-</7>
-
-![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 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 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">
+  <hr>
+  <img alt="Build Status" src="https://github.com/red-data-tools/YouPlot/workflows/test/badge.svg">
+  <a href="https://rubygems.org/gems/youplot/"><img alt="Gem Version" src="https://badge.fury.io/rb/youplot.svg"></a>
+  <a href="https://zenodo.org/badge/latestdoi/283230219"><img alt="DOI" src="https://zenodo.org/badge/283230219.svg"></a>
+  <a href="https://rubydoc.info/gems/youplot/"><img alt="Docs Stable" src="https://img.shields.io/badge/docs-stable-blue.svg"></a>
+  <a href="LICENSE.txt"><img alt="The MIT License" src="https://img.shields.io/badge/license-MIT-blue.svg"></a>
+  
+  YouPlot is a command line tool that draws plots on the terminal.
+
+  :bar_chart: Powered by [UnicodePlot](https://github.com/red-data-tools/unicode_plot.rb)
+</div>
 
 ## Installation
 
@@ -20,8 +20,9 @@ gem install youplot
 
 ## Quick Start
 
-* `cat data.tsv | uplot <command> [options]` or
-* `uplot <command> [options] <data.tsv>`
+<img alt="barplot" src="https://user-images.githubusercontent.com/5798442/101999903-d36a2d00-3d24-11eb-9361-b89116f44122.png" width=160> <img alt="histogram" src="https://user-images.githubusercontent.com/5798442/101999820-21cafc00-3d24-11eb-86db-e410d19b07df.png" width=160> <img alt="scatter" src="https://user-images.githubusercontent.com/5798442/101999827-27284680-3d24-11eb-9903-551857eaa69c.png" width=160> <img alt="density" src="https://user-images.githubusercontent.com/5798442/101999828-2abbcd80-3d24-11eb-902c-2f44266fa6ae.png" width=160> <img alt="boxplot" src="https://user-images.githubusercontent.com/5798442/101999830-2e4f5480-3d24-11eb-8891-728c18bf5b35.png" width=160>
+
+`uplot <command> [options] <data.tsv>`
 
 ### barplot
 
@@ -33,7 +34,7 @@ curl -sL https://git.io/ISLANDScsv \
 ```
 
 <p align="center">
-<img alt="barplot" src="https://user-images.githubusercontent.com/5798442/101999903-d36a2d00-3d24-11eb-9361-b89116f44122.png">
+  <img alt="barplot" src="https://user-images.githubusercontent.com/5798442/101999903-d36a2d00-3d24-11eb-9361-b89116f44122.png">
 </p>
 
 ### histogram
@@ -100,57 +101,41 @@ curl -sL https://git.io/IRIStsv \
 
 ### count
 
-In this example, YouPlot counts the number of chromosomes where the gene is located from the human gene annotation file and it creates 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
+| grep -v '#' | grep 'gene' | cut -f1 \
+| uplot count -t "The number of human gene annotations per chromosome"  -c blue
 ```
 
 <p align="center">
   <img alt="count" src="https://user-images.githubusercontent.com/5798442/101999832-30b1ae80-3d24-11eb-96fe-e5000bed1f5c.png">
 </p>
 
+In this example, YouPlot counts the number of chromosomes where genes are located. 
+* [GENCODE - Human Release](https://www.gencodegenes.org/human/)
+
 Note: `count` is not very fast because it runs in a Ruby script.
 This is fine in most cases, as long as the data size is small. 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
+| sort | uniq -c | sort -nrk1 \
+| uplot bar --fmt yx -d ' ' -t "The number of human gene annotations per chromosome"  -c blue
 ```
 
 ## Usage
 
-### Why YouPlot?
-
-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?
+### Commands
 
 `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` |
-
-### 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.
+| 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 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.
-
-### What types of plots are available?
+### Subcommands
 
 The following sub-commands are available.
 
@@ -163,67 +148,87 @@ The following sub-commands are available.
 | scatter   | s     | draw a scatter plot                    |
 | density   | d     | draw a density plot                    |
 | boxplot   | box   | draw a horizontal boxplot              |
+|           |       |                                        |
+| count     | c     | draw a barplot based on the number of occurrences (slow) |
+|           |       |                                        |
+| colors    | color | show the list of available colors      |
 
-See Quick Start for `count`.
+### Output the plot
 
-| command   | short | how it works                                             |
-|-----------|-------|----------------------------------------------------------|
-| count     | c     |  draw a barplot based on the number of occurrences (slow) |
+* `-o`
+  * By default, the plot is output to **standard error output**.
+  * If you want to output to standard input, Use hyphen ` -o -` or no argument `uplot s -o | `.
 
-### What if the header line is included?
+### Output the input data
 
-If your input data contains a header line, you need to specify the `-H` option.
+* `-O`
+  * By default, the input data is not shown anywhere.
+  * If you want to pass the input data directly to the standard output, Use hyphen `-O -` or no argument `uplot s -O |`.
+  * This is useful when passing data to a subsequent pipeline.
 
-### How to specify the delimiter?
+### Header
 
-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.
+* `-H`
+  * If input data contains a header line, you need to specify the `-H` option.
 
-### Is there a way to specify a column as the x-axis or y-axis?
+### Delimiter
 
-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.
+* `-d`
+  * You do not need to use `-d` option for tab-delimited text since the default value is tab.
+  * To specify a blank space, you can use `uplot bar -d ' ' data.txt`. 
 
-### How to plot real-time data?
+### Real-time data
 
-Experimental progressive mode is currently under development.
+* `-p` `--progress`
+  * Experimental progressive mode is currently under development.
+  * `ruby -e 'loop{puts rand(100)}' | uplot line --progress`
 
-```sh
-ruby -e 'loop{puts rand(100)}' | uplot line --progress
-```
+### Show detailed options for subcommands
 
-### How to view detailed command line options?
+* `--help`
+  * The `--help` option will show more detailed options for each subcommand.
+  * `uplot hist --help`
 
-Use `--help` to print command-specific options.
+### Set columns as x-axis or y-axis
 
-`uplot hist --help`
+* 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. 
 
-```
-Usage: uplot histogram [options] <in.tsv>
+* `--fmt`
+  * `--fmt xyy` `--fmt xyxy` `--fmt yx` options give you a few more choices. See `youplot <command> --help` for more details. 
+  * The fmt option may be renamed in the future. 
+  * The `-x` and `-y` options might be used to specify columns in the future.
 
-Options for histogram:
-        --symbol VAL         character to be used to plot the bars
-        --closed VAL         side of the intervals to be closed [left]
-    -n, --nbins VAL          approximate number of bins
+* Use `awk '{print $2, $1}'` to swap columns. Use `paste` to concatenate series.
 
-Options:
-...
-```
+### Categorical data
 
-### How to view the list of available colors?
+* With GNU datamash, you can manage to handle categorized data. 
+  * `cat test/fixtures/iris.csv | sed '/^$/d' | datamash --header-in --output-delimiter=: -t, -g5 collapse 3,4 | cut -f2-3 -d: | sed 's/:/\n/g' | uplot s -d, -T --fmt xyxy`
+  * This is not so easy...
 
-```sh
-uplot colors
-```
+### Time series
+
+* Not yet supported.
+
+## Tools that are useful to use with YouPlot
+
+* [csvtk](https://github.com/shenwei356/csvtk)
+* [GNU datamash](https://www.gnu.org/software/datamash/)
+* [awk](https://www.gnu.org/software/gawk/)
+* [xsv](https://github.com/BurntSushi/xsv)
 
 ## Contributing
 
-YouPlot is a library under development, so even small improvements like typofix are welcome! Please feel free to send us your pull requests.
+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/kojix2/youplot/issues)
-* Fix bugs and [submit pull requests](https://github.com/kojix2/youplot/pulls)
+* [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
 
@@ -233,11 +238,11 @@ 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
+bundle exec exe/uplot      # Run youplot (Try out the edited 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 +1,46 @@
 # 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'
 
+# If the line color is specified as a number, the program will display an error
+# message to the user and exit. Remove this patch when UnicodePlot is improved.
+
+module UnicodePlot
+  class << self
+    alias lineplot_original lineplot
+    def lineplot(*args, **kw)
+      if kw[:color].is_a? Numeric
+        warn <<~EOS
+          YouPlot: Line colors cannot be specified by numerical values.
+
+          For more information, please see the following issue.
+          https://github.com/red-data-tools/unicode_plot.rb/issues/34
+        EOS
+        YouPlot.run_as_executable ? exit(1) : raise(Error)
+      end
+      lineplot_original(*args, **kw)
+    end
+  end
+end
+
 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
@@ -39,7 +63,7 @@ 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)
@@ -47,7 +71,7 @@ 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)
@@ -57,7 +81,7 @@ 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'
@@ -75,7 +99,7 @@ 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
 
@@ -94,27 +118,26 @@ 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
 
       def plot_xyxy(data, method1, params)
         headers = data.headers
-        series = data.series
+        series2 = data.series
+                      .map { |s| s.map(&:to_f) }
+                      .each_slice(2).to_a
         method2 = get_method2(method1)
-        series.map! { |s| s.map(&:to_f) }
-        series2 = series.each_slice(2).to_a
-        series = nil
         params.name ||= headers[0] if headers
         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
@@ -152,13 +175,13 @@ 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
@@ -179,7 +202,7 @@ module YouPlot
         series = data.series
         if series.size == 1
           warn <<~EOS
-            youplot: There is only one series of input data. Please check the delimiter.
+            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

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))
@@ -59,23 +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]
 
+      # 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
 
@@ -95,15 +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
@@ -111,7 +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
@@ -134,7 +169,7 @@ module YouPlot
     def output_data(input)
       # Pass the input to subsequent pipelines
       case options[:pass]
-      when IO
+      when IO, StringIO
         options[:pass].print(input)
       else
         if options[:pass]
@@ -147,9 +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
@@ -158,7 +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?