youplot 0.3.2 → 0.4.1

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data/README.md

@@ -1,8 +1,10 @@
-![Logo](https://user-images.githubusercontent.com/5798442/102004318-ec89d280-3d52-11eb-8608-d890b42593f1.png)
+<p align="center">
+  <img src="logo.svg" width="60%" height="60%" />
+</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)
+[![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)
 
@@ -18,7 +20,8 @@ gem install youplot
 
 ## Quick Start
 
-`cat data.tsv | uplot <command> [options]`
+* `cat data.tsv | uplot <command> [options]` or
+* `uplot <command> [options] <data.tsv>`
 
 ### barplot
 
@@ -29,7 +32,9 @@ curl -sL https://git.io/ISLANDScsv \
 | uplot bar -d, -t "Areas of the World's Major Landmasses"
 ```
 
-![barplot](https://user-images.githubusercontent.com/5798442/101999903-d36a2d00-3d24-11eb-9361-b89116f44122.png)
+<p align="center">
+<img alt="barplot" src="https://user-images.githubusercontent.com/5798442/101999903-d36a2d00-3d24-11eb-9361-b89116f44122.png">
+</p>
 
 ### histogram
 
@@ -40,7 +45,10 @@ 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)
+
+<p align="center">
+  <img alt="histogram" src="https://user-images.githubusercontent.com/5798442/101999820-21cafc00-3d24-11eb-86db-e410d19b07df.png">
+</p>
 
 ### lineplot
 
@@ -50,7 +58,9 @@ curl -sL https://git.io/AirPassengers \
 | uplot line -d, -w 50 -h 15 -t AirPassengers --xlim 1950,1960 --ylim 0,600
 ```
 
-![lineplot](https://user-images.githubusercontent.com/5798442/101999825-24c5ec80-3d24-11eb-99f4-c642e8d221bc.png)
+<p align="center">
+  <img alt="lineplot" src="https://user-images.githubusercontent.com/5798442/101999825-24c5ec80-3d24-11eb-99f4-c642e8d221bc.png">
+</p>
 
 ### scatter
 
@@ -60,7 +70,9 @@ curl -sL https://git.io/IRIStsv \
 | uplot scatter -H -t IRIS
 ```
 
-![scatter](https://user-images.githubusercontent.com/5798442/101999827-27284680-3d24-11eb-9903-551857eaa69c.png)
+<p align="center">
+  <img alt="scatter" src="https://user-images.githubusercontent.com/5798442/101999827-27284680-3d24-11eb-9903-551857eaa69c.png">
+</p>
 
 ### density
 
@@ -70,7 +82,9 @@ curl -sL https://git.io/IRIStsv \
 | uplot density -H -t IRIS
 ```
 
-![density](https://user-images.githubusercontent.com/5798442/101999828-2abbcd80-3d24-11eb-902c-2f44266fa6ae.png)
+<p align="center">
+  <img alt="density" src="https://user-images.githubusercontent.com/5798442/101999828-2abbcd80-3d24-11eb-902c-2f44266fa6ae.png">
+</p>
 
 ### boxplot
 
@@ -80,28 +94,32 @@ curl -sL https://git.io/IRIStsv \
 | uplot boxplot -H -t IRIS
 ```
 
-![boxplot](https://user-images.githubusercontent.com/5798442/101999830-2e4f5480-3d24-11eb-8891-728c18bf5b35.png)
+<p align="center">
+  <img alt="boxplot" src="https://user-images.githubusercontent.com/5798442/101999830-2e4f5480-3d24-11eb-8891-728c18bf5b35.png">
+</p>
 
 ### 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.
+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
 ```
 
-![count](https://user-images.githubusercontent.com/5798442/101999832-30b1ae80-3d24-11eb-96fe-e5000bed1f5c.png)
+<p align="center">
+  <img alt="count" src="https://user-images.githubusercontent.com/5798442/101999832-30b1ae80-3d24-11eb-96fe-e5000bed1f5c.png">
+</p>
 
 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.
+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}' \
+| sort | uniq -c | sort -nrk2 | awk '{print $2,$1}' \
 | uplot bar -d ' ' -t "The number of human gene annotations per chromosome"  -c blue
 ```
 
@@ -109,32 +127,33 @@ cat gencode.v35.annotation.gff3 | grep -v '#' | grep 'gene' | cut -f1 \
 
 ### Why 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. 
+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?
 
-By default, the plot is output to *standard error output*. 
+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.
+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?
 
-The following sub-commands are available
+The following sub-commands are available.
 
 | command   | short | how it works                           |
 |-----------|-------|----------------------------------------|
@@ -150,9 +169,39 @@ See Quick Start for `count`.
 
 | command   | short | how it works                                             |
 |-----------|-------|----------------------------------------------------------|
-| count     | c     |  draw a baplot based on the number of occurrences (slow) |
+| count     | c     |  draw a barplot based on the number of occurrences (slow) |
+
+### What if the header line is included?
+
+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.
+
+### Is there a way to specify a column as the x-axis or y-axis?
+
+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 view detailed command line options
+### How to plot real-time data?
+
+Experimental progressive mode is currently under development.
+
+```sh
+ruby -e 'loop{puts rand(100)}' | uplot line --progress
+```
+
+### How to view detailed command line options?
 
 Use `--help` to print command-specific options.
 
@@ -163,7 +212,7 @@ 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:
@@ -178,22 +227,32 @@ uplot colors
 
 ## Contributing
 
+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)
 * 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
+
+* [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
+
 ## 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_reader'
-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