youplot 0.4.5 → 0.5.0

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@@ -1,7 +1,7 @@
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data/LICENSE.txt

@@ -1,6 +1,7 @@
 The MIT License (MIT)
 
 Copyright (c) 2020 kojix2
+Copyright (c) 2025 Red Data Tools
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

data/README.md

@@ -1,9 +1,8 @@
 <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://github.com/red-data-tools/YouPlot/actions/workflows/ci.yml"><img alt="Build Status" src="https://github.com/red-data-tools/YouPlot/workflows/test/badge.svg"></a>
   <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>
   
@@ -14,10 +13,30 @@
 
 ## Installation
 
+```
+brew install youplot
+```
+
 ```
 gem install youplot
 ```
 
+```
+nix shell nixpkgs#youplot
+```
+
+```
+guix install youplot
+```
+
+```
+conda install -c conda-forge ruby
+conda install -c conda-forge compilers
+gem install youplot
+```
+
+:crystal_ball: [YouPlot2](https://github.com/red-data-tools/YouPlot2) - Experimental project with pre-built binaries
+
 ## Quick Start
 
 <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>
@@ -37,13 +56,19 @@ curl -sL https://git.io/ISLANDScsv \
   <img alt="barplot" src="https://user-images.githubusercontent.com/5798442/101999903-d36a2d00-3d24-11eb-9361-b89116f44122.png">
 </p>
 
+For offline users: sorts files in a directory by size and shows a bar graph.
+
+```sh
+ls -l | awk '{print $9, $5}' | sort -nk 2 | uplot bar -d ' '
+```
+
 ### histogram
 
 ```sh
 echo -e "from numpy import random;" \
         "n = random.randn(10000);"  \
         "print('\\\n'.join(str(i) for i in n))" \
-| python \
+| python3 \
 | uplot hist --nbins 20
 ```
 
@@ -63,6 +88,17 @@ curl -sL https://git.io/AirPassengers \
   <img alt="lineplot" src="https://user-images.githubusercontent.com/5798442/101999825-24c5ec80-3d24-11eb-99f4-c642e8d221bc.png">
 </p>
 
+For offline users: calculates sin values from 0 to 2*pi and plots a sine wave.
+
+```sh
+python3 - <<'PY' | uplot line
+from math import sin, pi
+
+for i in range(101):
+    print(f"{i*pi/50}\t{sin(i*pi/50)}")
+PY
+```
+
 ### scatter
 
 ```sh
@@ -75,6 +111,13 @@ curl -sL https://git.io/IRIStsv \
   <img alt="scatter" src="https://user-images.githubusercontent.com/5798442/101999827-27284680-3d24-11eb-9903-551857eaa69c.png">
 </p>
 
+
+For offline users:
+
+```sh
+cat test/fixtures/iris.csv | cut -f1-4 -d, | uplot scatter -H -d, -t IRIS
+```
+
 ### density
 
 ```sh
@@ -87,6 +130,12 @@ curl -sL https://git.io/IRIStsv \
   <img alt="density" src="https://user-images.githubusercontent.com/5798442/101999828-2abbcd80-3d24-11eb-902c-2f44266fa6ae.png">
 </p>
 
+For offline users:
+
+```sh
+cat test/fixtures/iris.csv | cut -f1-4 -d, | uplot density -H -d, -t IRIS
+```
+
 ### boxplot
 
 ```sh
@@ -99,8 +148,22 @@ curl -sL https://git.io/IRIStsv \
   <img alt="boxplot" src="https://user-images.githubusercontent.com/5798442/101999830-2e4f5480-3d24-11eb-8891-728c18bf5b35.png">
 </p>
 
+For offline users:
+
+```sh
+cat test/fixtures/iris.csv | cut -f1-4 -d, | uplot boxplot -H -d, -t IRIS
+```
+
 ### count
 
+Count processes by user ID.
+
+```sh
+ps aux | awk '{print $1}' | uplot count
+```
+
+Count the number of chromosomes where genes are located. 
+
 ```sh
 cat gencode.v35.annotation.gff3 \
 | grep -v '#' | grep 'gene' | cut -f1 \
@@ -111,7 +174,6 @@ cat gencode.v35.annotation.gff3 \
   <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.
@@ -130,7 +192,7 @@ cat gencode.v35.annotation.gff3 | grep -v '#' | grep 'gene' | cut -f1 \
 `uplot` is the shortened form of `youplot`. You can use either.
 
 | 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 |
@@ -139,25 +201,25 @@ cat gencode.v35.annotation.gff3 | grep -v '#' | grep 'gene' | cut -f1 \
 
 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              |
-|           |       |                                        |
+| 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                                |
+|           |       |                                                          |
 | count     | c     | draw a barplot based on the number of occurrences (slow) |
-|           |       |                                        |
-| colors    | color | show the list of available colors      |
+|           |       |                                                          |
+| colors    | color | show the list of available colors                        |
 
 ### Output the plot
 
 * `-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 | `.
+  * If you want to output to standard output, Use hyphen ` -o -` or no argument `uplot s -o | `.
 
 ### Output the input data
 
@@ -240,13 +302,14 @@ Please feel free to send us your pull requests.
 
 ### Development
 
+Fork the main repository by clicking the Fork button.
+
 ```sh
-# 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
-bundle exec exe/uplot      # Run youplot (Try out the edited code)
+bundle install
+bundle exec rake test
+bundle exec rake install
+bundle exec exe/uplot
 ```
 
     Do you need commit rights to my repository?
@@ -255,7 +318,7 @@ bundle exec exe/uplot      # Run youplot (Try out the edited code)
 
 ### Acknowledgements
 
-* [sampo grafiikka](https://jypg.net/sampo_grafiikka) - Project logo creation
+* [sampo grafiikka](https://lepo.sampo-grafiikka.com/) - Project logo creation
 * [yutaas](https://github.com/yutaas) - English proofreading
 
 ## License

data/lib/youplot/aggregation.rb

@@ -0,0 +1,140 @@
+# frozen_string_literal: true
+
+module YouPlot
+  module Aggregation
+    module_function
+
+    def count_values(arr, tally: true, reverse: false)
+      # tally was added in Ruby 2.7
+      result = \
+        if tally && Enumerable.method_defined?(:tally)
+          arr.tally
+        else
+          # value_counts Enumerable::Statistics
+          arr.value_counts(dropna: false)
+        end
+
+      sort_cache = {}
+
+      # sorting
+      result = result.sort do |a, b|
+        # compare values
+        r = b[1] <=> a[1]
+        # If the values are the same, compare by name
+        r = natural_compare(a[0], b[0], sort_cache) if r.zero?
+        r
+      end
+
+      # --reverse option
+      result.reverse! if reverse
+
+      # prepare for barplot
+      result.transpose
+    end
+
+    # Natural order comparison for tie-breaking when counts are equal.
+    # Fast paths handle text-only and pure numeric labels.
+    # Mixed labels still use chunked comparison (e.g. "chr1" vs "chr10").
+    def natural_compare(a, b, cache = nil)
+      aa = natural_sort_key(a, cache)
+      bb = natural_sort_key(b, cache)
+
+      # Fast path: both labels are text-only, so plain string comparison is enough.
+      return aa[:string] <=> bb[:string] if aa[:type] == :text && bb[:type] == :text
+
+      # Fast path: both labels are pure numbers, so compare numerically first.
+      if aa[:type] == :numeric && bb[:type] == :numeric
+        r = aa[:numeric] <=> bb[:numeric]
+        return r unless r.zero?
+
+        # Tiebreaker for equivalent numeric values (e.g. "1" and "01")
+        return aa[:string] <=> bb[:string]
+      end
+
+      # Fallback path: at least one label mixes text and digits.
+      ta = ensure_natural_tokens(aa)
+      tb = ensure_natural_tokens(bb)
+      max = [ta.size, tb.size].max
+
+      0.upto(max - 1) do |i|
+        xa = ta[i]
+        xb = tb[i]
+
+        return -1 if xa.nil?
+        return 1 if xb.nil?
+
+        r = if xa[0] == :num && xb[0] == :num
+              compare_integer_strings(xa[1], xb[1])
+            else
+              xa[1] <=> xb[1]
+            end
+
+        return r unless r.zero?
+      end
+
+      aa[:string] <=> bb[:string]
+    end
+
+    # Classifies a value for natural sorting and caches the result per label.
+    def natural_sort_key(value, cache = nil)
+      str = value.to_s
+      return cache[str] if cache && cache.key?(str)
+
+      key = if str.match?(/\d/)
+              numeric = parse_numeric(str)
+              if numeric
+                # Pure numeric labels get a dedicated fast path.
+                { type: :numeric, string: str, numeric: numeric }
+              else
+                # Mixed labels fall back to chunked natural comparison.
+                { type: :mixed, string: str, tokens: nil }
+              end
+            else
+              # Text-only labels get a dedicated fast path.
+              { type: :text, string: str, tokens: nil }
+            end
+
+      cache ? cache[str] = key : key
+    end
+
+    # Memoizes token pairs for fallback chunked comparison.
+    def ensure_natural_tokens(key)
+      key[:tokens] ||= natural_tokens(key[:string])
+    end
+
+    # Parses a string as a numeric value if it matches pure number format.
+    # Returns Float or nil.
+    def parse_numeric(str)
+      return nil unless str.match?(/\A[+-]?(?:\d+(?:\.\d+)?|\.\d+)\z/)
+
+      str.to_f
+    end
+
+    # Splits a string into [type, token] pairs for natural comparison.
+    # Type is :num for digit-only chunks, :text for anything else.
+    # E.g. "chr10" => [[:text, "chr"], [:num, "10"]]
+    def natural_tokens(str)
+      str.scan(/\d+|\D+/).map do |tok|
+        kind = tok.match?(/\A\d+\z/) ? :num : :text
+        [kind, tok]
+      end
+    end
+
+    # Compares two numeric strings, handling leading zeros.
+    # Order: by length (sans leading zeros), then numeric value, then original.
+    def compare_integer_strings(a, b)
+      aa = a.sub(/\A0+/, '')
+      bb = b.sub(/\A0+/, '')
+      aa = '0' if aa.empty?
+      bb = '0' if bb.empty?
+
+      r = aa.length <=> bb.length
+      return r unless r.zero?
+
+      r = aa <=> bb
+      return r unless r.zero?
+
+      a <=> b
+    end
+  end
+end

data/lib/youplot/backends/unicode_plot.rb

@@ -3,7 +3,7 @@
 # UnicodePlot - Plot your data by Unicode characters
 # https://github.com/red-data-tools/unicode_plot.rb
 
-require_relative 'processing'
+require_relative '../aggregation'
 require 'unicode_plot'
 
 # If the line color is specified as a number, the program will display an error
@@ -40,13 +40,14 @@ module YouPlot
         series = data.series
         # `uplot count`
         if count
-          series = Processing.count_values(series[0], reverse: reverse)
+          series = YouPlot::Aggregation.count_values(series[0], reverse: reverse)
           params.title = headers[0] if headers
         end
         if series.size == 1
           # 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 }
+          raw_values = series[0]
           values = series[0].map(&:to_f)
         else
           # If there are 2 or more series...
@@ -61,11 +62,28 @@ module YouPlot
           end
           params.title ||= headers[y_col] if headers
           labels = series[x_col]
-          values = series[y_col].map(&:to_f)
+          raw_values = series[y_col]
+          values = if count
+                     series[y_col].map(&:to_i)
+                   else
+                     series[y_col].map(&:to_f)
+                   end
         end
+        values = values.map(&:to_i) if count || integer_display_values?(values, raw_values)
         ::UnicodePlot.barplot(labels, values, **params.to_hc)
       end
 
+      # True only for integer literals: "3" => true, "3.0" => false.
+      def integer_display_values?(values, raw_values)
+        values.all? { |v| v.finite? && v == v.to_i } &&
+          raw_values.all? { |v| integer_literal?(v) }
+      end
+
+      def integer_literal?(value)
+        # Matches "3" and "-12", but not "3.0".
+        value.to_s.match?(/\A[+-]?\d+\z/)
+      end
+
       def histogram(data, params)
         headers = data.headers
         series = data.series
@@ -200,27 +218,37 @@ module YouPlot
 
       def check_series_size(data, fmt)
         series = data.series
-        if series.size == 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 <<~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
+        raise_if_single_series(data, series) if series.size == 1
+        raise_if_odd_series_for_xyxy(data, fmt, series)
+      end
+
+      def raise_if_single_series(data, series)
+        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
+        raise_plot_error
+      end
+
+      def raise_if_odd_series_for_xyxy(data, fmt, series)
+        return unless fmt == 'xyxy'
+        return if series.size.even?
+
+        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
+        raise_plot_error
+      end
+
+      def raise_plot_error
+        # NOTE: Error messages cannot be colored.
+        YouPlot.run_as_executable ? exit(1) : raise(Error)
       end
     end
   end