mirror of
https://github.com/red-data-tools/YouPlot.git
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200 lines
6.3 KiB
Markdown
200 lines
6.3 KiB
Markdown
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[](https://badge.fury.io/rb/youplot)
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[](https://rubydoc.info/gems/youplot)
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[](LICENSE.txt)
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[](https://zenodo.org/badge/latestdoi/283230219)
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YouPlot is a command line tool for Unicode Plotting working with data from standard stream.
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:bar_chart: Powered by [UnicodePlot](https://github.com/red-data-tools/unicode_plot.rb)
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## Installation
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```
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gem install youplot
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```
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## Quick Start
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`cat data.tsv | uplot <command> [options]`
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### barplot
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```sh
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curl -sL https://git.io/ISLANDScsv \
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| sort -nk2 -t, \
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| tail \
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| uplot bar -d, -t "Areas of the World's Major Landmasses"
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```
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### histogram
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```sh
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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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```
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### lineplot
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```sh
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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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```
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### scatter
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```sh
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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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```
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### density
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```sh
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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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```
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### boxplot
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```sh
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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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```
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### count
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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.
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* https://www.gencodegenes.org/human/
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```sh
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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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```
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Note: `count` is not very fast because it runs in a Ruby script.
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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.
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```sh
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cat gencode.v35.annotation.gff3 | grep -v '#' | grep 'gene' | cut -f1 \
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|sort | uniq -c | sort -nrk2 | awk '{print $2,$1}' \
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| uplot bar -d ' ' -t "The number of human gene annotations per chromosome" -c blue
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```
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## Usage
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### Why YouPlot?
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Wouldn't it be a bit of pain to have to run R, Python, Julia, gnuplot or whatever REPL just to check your data?
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YouPlot is a command line tool for this purpose. With YouPlot, you can continue working without leaving your terminal and shell.
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### how to use YouPlot?
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`uplot` is the shortened form of `youplot`. You can use either.
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|-----------------------------------|------------------------------------------------|
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| Reads data from standard input | `cat data.tsv \| uplot <command> [options]` |
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| Reads data from files | `uplot <command> [options] data.tsv ...` |
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| Outputs data from stdin to stdout | `pipeline1 \| uplot <command> -O \| pipeline2` |
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### Where to output the plot?
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By default, the plot is output to *standard error output*.
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The output file or stream for the plot can be specified with the `-o` option.
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### Where to output the input data?
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By default, the input data is not output anywhere.
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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.
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### What types of plots are available?
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The following sub-commands are available
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| command | short | how it works |
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|-----------|-------|----------------------------------------|
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| barplot | bar | draw a horizontal barplot |
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| histogram | hist | draw a horizontal histogram |
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| lineplot | line | draw a line chart |
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| lineplots | lines | draw a line chart with multiple series |
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| scatter | s | draw a scatter plot |
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| density | d | draw a density plot |
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| boxplot | box | draw a horizontal boxplot |
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See Quick Start for `count`.
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| command | short | how it works |
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|-----------|-------|----------------------------------------------------------|
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| count | c | draw a baplot based on the number of occurrences (slow) |
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### How to view detailed command line options
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Use `--help` to print command-specific options.
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`uplot hist --help`
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```
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Usage: uplot histogram [options] <in.tsv>
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Options for histogram:
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--symbol VAL character to be used to plot the bars
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--closed VAL
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-n, --nbins VAL approximate number of bins
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Options:
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...
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```
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### How to view the list of available colors?
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```sh
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uplot colors
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```
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## Contributing
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* [Report bugs](https://github.com/kojix2/youplot/issues)
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* Fix bugs and [submit pull requests](https://github.com/kojix2/youplot/pulls)
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* Write, clarify, or fix documentation
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* Suggest or add new features
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### Development
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```sh
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git clone https://github.com/your_name/GR.rb # Clone the Git repo
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cd GR.rb
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bundle install # Install the gem dependencies
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bundle exec rake test # Run the test
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bundle exec rake install # Installation from source code
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```
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## License
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[MIT License](https://opensource.org/licenses/MIT).
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