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File: README
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— Documentation by YARD 0.9.28
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<span class="title">File: README</span>
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<img src="logo.svg">
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<hr>
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<img alt="Build Status" src="https://github.com/red-data-tools/YouPlot/workflows/test/badge.svg">
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<a href="https://rubygems.org/gems/youplot/"><img alt="Gem Version" src="https://badge.fury.io/rb/youplot.svg"></a>
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<a href="https://zenodo.org/badge/latestdoi/283230219"><img alt="DOI" src="https://zenodo.org/badge/283230219.svg"></a>
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<a href="https://rubydoc.info/gems/youplot/"><img alt="Docs Stable" src="https://img.shields.io/badge/docs-stable-blue.svg"></a>
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<a href="LICENSE.txt"><img alt="The MIT License" src="https://img.shields.io/badge/license-MIT-blue.svg"></a>
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YouPlot is a command line tool that draws plots on the terminal.
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:bar_chart: Powered by [UnicodePlot](https://github.com/red-data-tools/unicode_plot.rb)
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</div>
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<h2 id="label-Installation">Installation</h2>
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<pre class="code ruby"><code class="ruby"><span class='id identifier rubyid_gem'>gem</span> <span class='id identifier rubyid_install'>install</span> <span class='id identifier rubyid_youplot'>youplot</span>
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</code></pre>
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<h2 id="label-Quick+Start">Quick Start</h2>
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<p><img alt=“barplot” src=“<img src="https://user-images.githubusercontent.com/5798442/101999903-d36a2d00-3d24-11eb-9361-b89116f44122.png" />” width=160> <img alt=“histogram” src=“<img src="https://user-images.githubusercontent.com/5798442/101999820-21cafc00-3d24-11eb-86db-e410d19b07df.png" />” width=160> <img alt=“scatter” src=“<img src="https://user-images.githubusercontent.com/5798442/101999827-27284680-3d24-11eb-9903-551857eaa69c.png" />” width=160> <img alt=“density” src=“<img src="https://user-images.githubusercontent.com/5798442/101999828-2abbcd80-3d24-11eb-902c-2f44266fa6ae.png" />” width=160> <img alt=“boxplot” src=“<img src="https://user-images.githubusercontent.com/5798442/101999830-2e4f5480-3d24-11eb-8891-728c18bf5b35.png" />” width=160></p>
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<p><code>uplot <command> [options] <data.tsv></code></p>
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<h3 id="label-barplot">barplot</h3>
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<pre class="code ruby"><code class="ruby">curl -sL https://git.io/ISLANDScsv \
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| sort -nk2 -t, \
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| tail -n15 \
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| uplot bar -d, -t "Areas of the World's Major Landmasses"
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</code></pre>
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<p align="center">
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<img alt="barplot" src="https://user-images.githubusercontent.com/5798442/101999903-d36a2d00-3d24-11eb-9361-b89116f44122.png">
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</p>
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<h3 id="label-histogram">histogram</h3>
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<pre class="code ruby"><code class="ruby">echo -e "from numpy import random;" \
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"n = random.randn(10000);" \
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"print('\\\n'.join(str(i) for i in n))" \
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| python \
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| uplot hist --nbins 20
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</code></pre>
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<p align="center">
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<img alt="histogram" src="https://user-images.githubusercontent.com/5798442/101999820-21cafc00-3d24-11eb-86db-e410d19b07df.png">
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</p>
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<h3 id="label-lineplot">lineplot</h3>
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<pre class="code ruby"><code class="ruby">curl -sL https://git.io/AirPassengers \
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| cut -f2,3 -d, \
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| uplot line -d, -w 50 -h 15 -t AirPassengers --xlim 1950,1960 --ylim 0,600
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</code></pre>
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<p align="center">
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<img alt="lineplot" src="https://user-images.githubusercontent.com/5798442/101999825-24c5ec80-3d24-11eb-99f4-c642e8d221bc.png">
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</p>
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<h3 id="label-scatter">scatter</h3>
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<pre class="code ruby"><code class="ruby">curl -sL https://git.io/IRIStsv \
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| cut -f1-4 \
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| uplot scatter -H -t IRIS
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</code></pre>
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<p align="center">
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<img alt="scatter" src="https://user-images.githubusercontent.com/5798442/101999827-27284680-3d24-11eb-9903-551857eaa69c.png">
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</p>
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<h3 id="label-density">density</h3>
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<pre class="code ruby"><code class="ruby">curl -sL https://git.io/IRIStsv \
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| cut -f1-4 \
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| uplot density -H -t IRIS
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</code></pre>
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<p align="center">
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<img alt="density" src="https://user-images.githubusercontent.com/5798442/101999828-2abbcd80-3d24-11eb-902c-2f44266fa6ae.png">
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</p>
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<h3 id="label-boxplot">boxplot</h3>
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<pre class="code ruby"><code class="ruby">curl -sL https://git.io/IRIStsv \
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| cut -f1-4 \
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| uplot boxplot -H -t IRIS
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</code></pre>
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<p align="center">
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<img alt="boxplot" src="https://user-images.githubusercontent.com/5798442/101999830-2e4f5480-3d24-11eb-8891-728c18bf5b35.png">
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</p>
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<h3 id="label-count">count</h3>
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<pre class="code ruby"><code class="ruby">cat gencode.v35.annotation.gff3 \
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| grep -v '#' | grep 'gene' | cut -f1 \
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| uplot count -t "The number of human gene annotations per chromosome" -c blue
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</code></pre>
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<p align="center">
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<img alt="count" src="https://user-images.githubusercontent.com/5798442/101999832-30b1ae80-3d24-11eb-96fe-e5000bed1f5c.png">
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</p>
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<p>In this example, YouPlot counts the number of chromosomes where genes are located. * <a href="https://www.gencodegenes.org/human/">GENCODE - Human Release</a></p>
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<p>Note: <code>count</code> 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.</p>
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<pre class="code ruby"><code class="ruby">cat gencode.v35.annotation.gff3 | grep -v '#' | grep 'gene' | cut -f1 \
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| sort | uniq -c | sort -nrk1 \
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| uplot bar --fmt yx -d ' ' -t "The number of human gene annotations per chromosome" -c blue
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</code></pre>
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<h2 id="label-Usage">Usage</h2>
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<h3 id="label-Commands">Commands</h3>
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<p><code>uplot</code> is the shortened form of <code>youplot</code>. You can use either.</p>
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<table role="table">
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<thead>
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<tr>
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<th>Command</th>
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<th>Description</th>
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</tr>
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</thead>
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<tbody>
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<tr>
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<td>‘cat data.tsv | uplot <command> [options]`</td>
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<td>Take input from stdin</td>
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</tr>
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<tr>
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<td>‘uplot <command> [options] data.tsv …`</td>
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<td>Take input from files</td>
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</tr>
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<tr>
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<td>‘pipeline1 | uplot <command> -O | pipeline2`</td>
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<td>Outputs data from stdin to stdout</td>
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</tr>
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</tbody>
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</table>
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<h3 id="label-Subcommands">Subcommands</h3>
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<p>The following sub-commands are available.</p>
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<table role="table">
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<thead>
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<tr>
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<th>command</th>
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<th>short</th>
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<th>how it works</th>
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</tr>
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</thead>
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<tbody>
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<tr>
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<td>barplot</td>
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<td>bar</td>
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<td>draw a horizontal barplot</td>
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</tr>
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<tr>
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<td>histogram</td>
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<td>hist</td>
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<td>draw a horizontal histogram</td>
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</tr>
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<tr>
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<td>lineplot</td>
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<td>line</td>
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<td>draw a line chart</td>
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</tr>
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<tr>
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<td>lineplots</td>
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<td>lines</td>
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<td>draw a line chart with multiple series</td>
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</tr>
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<tr>
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<td>scatter</td>
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<td>s</td>
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<td>draw a scatter plot</td>
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</tr>
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<tr>
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<td>density</td>
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<td>d</td>
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<td>draw a density plot</td>
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</tr>
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<tr>
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<td>boxplot</td>
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<td>box</td>
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<td>draw a horizontal boxplot</td>
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</tr>
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<tr>
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<td></td>
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<td></td>
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<td></td>
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</tr>
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<tr>
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<td>count</td>
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<td>c</td>
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<td>draw a barplot based on the number of occurrences (slow)</td>
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</tr>
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<tr>
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<td></td>
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<td></td>
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<td></td>
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</tr>
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<tr>
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<td>colors</td>
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<td>color</td>
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<td>show the list of available colors</td>
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</tr>
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</tbody>
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</table>
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<h3 id="label-Output+the+plot">Output the plot</h3>
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<ul><li>
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<p><code>-o</code></p>
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</li><li>
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<p>By default, the plot is output to <strong>standard error output</strong>.</p>
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</li><li>
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<p>If you want to output to standard input, Use hyphen <code>-o -</code> or no argument <code>uplot s -o |</code>.</p>
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</li></ul>
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<h3 id="label-Output+the+input+data">Output the input data</h3>
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<ul><li>
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<p><code>-O</code></p>
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</li><li>
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<p>By default, the input data is not shown anywhere.</p>
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</li><li>
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<p>If you want to pass the input data directly to the standard output, Use hyphen <code>-O -</code> or no argument <code>uplot s -O |</code>.</p>
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</li><li>
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<p>This is useful when passing data to a subsequent pipeline.</p>
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</li></ul>
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<h3 id="label-Header">Header</h3>
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<ul><li>
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<p><code>-H</code></p>
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</li><li>
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<p>If input data contains a header line, you need to specify the <code>-H</code> option.</p>
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</li></ul>
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<h3 id="label-Delimiter">Delimiter</h3>
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<ul><li>
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<p><code>-d</code></p>
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</li><li>
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<p>You do not need to use <code>-d</code> option for tab-delimited text since the default value is tab.</p>
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</li><li>
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<p>To specify a blank space, you can use <code>uplot bar -d ' ' data.txt</code>.</p>
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</li></ul>
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<h3 id="label-Real-time+data">Real-time data</h3>
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<ul><li>
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<p><code>-p</code> <code>--progress</code></p>
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</li><li>
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<p>Experimental progressive mode is currently under development.</p>
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</li><li>
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<p><code>ruby -e 'loop{puts rand(100)}' | uplot line --progress</code></p>
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</li></ul>
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<h3 id="label-Show+detailed+options+for+subcommands">Show detailed options for subcommands</h3>
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<ul><li>
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<p><code>--help</code></p>
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</li><li>
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<p>The <code>--help</code> option will show more detailed options for each subcommand.</p>
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</li><li>
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<p><code>uplot hist --help</code></p>
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</li></ul>
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<h3 id="label-Set+columns+as+x-axis+or+y-axis">Set columns as x-axis or y-axis</h3>
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<ul><li>
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<p>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.</p>
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</li><li>
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<p>If you pass only one column of data for <code>line</code> and <code>bar</code>, YouPlot will automatically use a sequential number starting from 1 as the X-axis.</p>
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</li><li>
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<p><code>--fmt</code></p>
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</li><li>
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<p><code>--fmt xyy</code> <code>--fmt xyxy</code> <code>--fmt yx</code> options give you a few more choices. See <code>youplot <command> --help</code> for more details.</p>
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</li><li>
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<p>The fmt option may be renamed in the future.</p>
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</li><li>
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<p>The <code>-x</code> and <code>-y</code> options might be used to specify columns in the future.</p>
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</li><li>
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<p>Use <code>awk '{print $2, $1}'</code> to swap columns. Use <code>paste</code> to concatenate series.</p>
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</li></ul>
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<h3 id="label-Categorical+data">Categorical data</h3>
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<ul><li>
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<p>With GNU datamash, you can manage to handle categorized data.</p>
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</li><li>
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<p><code>cat test/fixtures/iris.csv | sed '/^$/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</code></p>
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||
</li><li>
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||
<p>This is not so easy…</p>
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</li></ul>
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<h3 id="label-Time+series">Time series</h3>
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<ul><li>
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<p>Not yet supported.</p>
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</li></ul>
|
||
|
||
<h3 id="label-YouPlot+Configuration+-28youplotrc-29">YouPlot Configuration (youplotrc)</h3>
|
||
|
||
<p>You can specify default options in a configuration file in YAML format. For more information, enter the following command.</p>
|
||
|
||
<pre class="code ruby"><code class="ruby"><span class='id identifier rubyid_uplot'>uplot</span> <span class='op'>-</span><span class='op'>-</span><span class='id identifier rubyid_config'>config</span>
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||
</code></pre>
|
||
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||
<h2 id="label-Tools+that+are+useful+to+use+with+YouPlot">Tools that are useful to use with YouPlot</h2>
|
||
<ul><li>
|
||
<p><a href="https://github.com/shenwei356/csvtk">csvtk</a></p>
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||
</li><li>
|
||
<p><a href="https://www.gnu.org/software/datamash/">GNU datamash</a></p>
|
||
</li><li>
|
||
<p><a href="https://www.gnu.org/software/gawk/">awk</a></p>
|
||
</li><li>
|
||
<p><a href="https://github.com/BurntSushi/xsv">xsv</a></p>
|
||
</li></ul>
|
||
|
||
<h2 id="label-Contributing">Contributing</h2>
|
||
|
||
<p>YouPlot is a library under development, so even small improvements like typofix are welcome! Please feel free to send us your pull requests.</p>
|
||
<ul><li>
|
||
<p><a href="https://github.com/red-data-tools/YouPlot/issues">Report bugs</a></p>
|
||
</li><li>
|
||
<p>Fix bugs and <a href="https://github.com/red-data-tools/YouPlot/pulls">submit pull requests</a></p>
|
||
</li><li>
|
||
<p>Write, clarify, or fix documentation</p>
|
||
</li><li>
|
||
<p>English corrections by native speakers are welcome.</p>
|
||
</li><li>
|
||
<p>Suggest or add new features</p>
|
||
</li><li>
|
||
<p>Make a donation</p>
|
||
</li></ul>
|
||
|
||
<h3 id="label-Development">Development</h3>
|
||
|
||
<pre class="code ruby"><code class="ruby"># fork the main repository by clicking the Fork button.
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git clone https://github.com/your_name/YouPlot
|
||
bundle install # Install the gem dependencies
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bundle exec rake test # Run the test
|
||
bundle exec rake install # Installation from source code
|
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bundle exec exe/uplot # Run youplot (Try out the edited code)
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||
</code></pre>
|
||
|
||
<pre class="code ruby"><code class="ruby">Do you need commit rights to my repository?
|
||
Do you want to get admin rights and take over the project?
|
||
If so, please feel free to contact us.
|
||
</code></pre>
|
||
|
||
<h3 id="label-Acknowledgements">Acknowledgements</h3>
|
||
<ul><li>
|
||
<p><a href="https://jypg.net/sampo_grafiikka">sampo grafiikka</a> - Project logo creation</p>
|
||
</li><li>
|
||
<p><a href="https://github.com/yutaas">yutaas</a> - English proofreading</p>
|
||
</li></ul>
|
||
|
||
<h2 id="label-License">License</h2>
|
||
|
||
<p><a href="https://opensource.org/licenses/MIT">MIT License</a>.</p>
|
||
</div></div>
|
||
|
||
<div id="footer">
|
||
Generated on Thu Jan 5 03:56:28 2023 by
|
||
<a href="https://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
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0.9.28 (ruby-3.2.0).
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</div>
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</div>
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</body>
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</html> |