youplot 0.3.1 → 0.3.2
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- checksums.yaml +4 -4
- data/README.md +117 -66
- data/lib/youplot/backends/unicode_plot_backend.rb +13 -7
- data/lib/youplot/command.rb +79 -67
- data/lib/youplot/command/cmd_options.rb +18 -0
- data/lib/youplot/command/parser.rb +44 -35
- data/lib/youplot/command/{params.rb → plot_params.rb} +1 -1
- data/lib/youplot/version.rb +1 -1
- metadata +4 -3
checksums.yaml
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SHA256:
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metadata.gz:
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metadata.gz: ff7e21952a560421314ae80fc894a8c1321d27ad985f50d2cdc53f8b3306a5ba
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data.tar.gz: 5229cb0a38b73477ab91570dd0d04bf646c66d511fb6d5c8a12c09d64a08d1cf
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metadata.gz:
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metadata.gz: d8d28d4118af6be5d7b115a3341e2bc066821718d0367286c2dbb2d49f364ac241af1d75f8c0466f91761e7a1c1ccdab4693010f41389c2703a25a3b9b83c8a2
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data.tar.gz: ccc0b88ff329b9f002cb089f07ddfd9e3be8eed1a63a6c609df018efb1b25f3a92ff640ae22413e3271d051799cc009a090d8af1662b408282941e190da7f75b
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data/README.md
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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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gem install youplot
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```
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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 -n15 \
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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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| 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 -
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| cut -f1-4
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| uplot scatter -H -
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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 -
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| cut -
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| uplot
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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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| uplot
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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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Version: 0.2.7 (using UnicodePlot 0.0.4)
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Source: https://github.com/kojix2/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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barplot bar
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histogram hist
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lineplot line
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lineplots lines
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scatter s
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density d
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boxplot box
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colors show the list of available colors
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`uplot` is the shortened form of `youplot`. You can use either.
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| | |
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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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...
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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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@@ -152,17 +152,23 @@ module YouPlot
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end
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def colors(color_names = false)
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# FIXME
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s = String.new
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UnicodePlot::StyledPrinter::TEXT_COLORS.each do |k, v|
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s << v
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s << k.to_s
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unless color_names
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s << "\t"
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s << ' ●'
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end
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s << "\033[0m"
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s << "\t"
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end
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-
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s << "\n"
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def s.render(obj)
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obj.print(self)
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end
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s
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end
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def check_series_size(data, fmt)
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data/lib/youplot/command.rb
CHANGED
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Data = Struct.new(:headers, :series)
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class Command
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attr_accessor :params
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attr_reader :data, :
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attr_accessor :command, :params, :options
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attr_reader :data, :parser
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def initialize(argv = ARGV)
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@argv = argv
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@params = Params.new
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@parser = Parser.new
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@command = nil
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@params = nil
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@options = nil
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@backend = YouPlot::Backends::UnicodePlotBackend
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end
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def run
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parser.parse_options(@argv)
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command
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transpose = parser.transpose
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headers = parser.headers
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pass = parser.pass
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output = parser.output
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fmt = parser.fmt
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@encoding = parser.encoding
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@debug = parser.debug
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if command == :colors
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@backend.colors(parser.color_names)
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exit
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end
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@command ||= parser.command
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@options ||= parser.options
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@params ||= parser.params
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else
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if pass
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File.open(pass, 'w') do |f|
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f.print(input)
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end
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end
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if %i[colors color colours colour].include? @command
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plot = create_plot
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output_plot(plot)
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else
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# Sometimes the input file does not end with a newline code.
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while (input = Kernel.gets(nil))
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main(input)
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end
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end
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end
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private
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def main(input)
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output_data(input)
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@data = read_dsv(input)
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pp @data if options[:debug]
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plot = create_plot
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output_plot(plot)
|
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end
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def read_dsv(input)
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+
input = input.dup.force_encoding(options[:encoding]).encode('utf-8') if options[:encoding]
|
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+
DSVReader.input(input, options[:delimiter], options[:headers], options[:transpose])
|
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+
end
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-
File.open(output, 'w') do |f|
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plot.render(f)
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+
def create_plot
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+
case command
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when :bar, :barplot
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+
@backend.barplot(data, params, options[:fmt])
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+
when :count, :c
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@backend.barplot(data, params, count: true)
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when :hist, :histogram
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@backend.histogram(data, params)
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when :line, :lineplot
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@backend.line(data, params, options[:fmt])
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when :lines, :lineplots
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+
@backend.lines(data, params, options[:fmt])
|
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when :scatter, :s
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@backend.scatter(data, params, options[:fmt])
|
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when :density, :d
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@backend.density(data, params, options[:fmt])
|
|
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+
when :box, :boxplot
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+
@backend.boxplot(data, params)
|
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+
when :colors, :color, :colours, :colour
|
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|
+
@backend.colors(options[:color_names])
|
|
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|
+
else
|
|
81
|
+
raise "unrecognized plot_type: #{command}"
|
|
82
|
+
end
|
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83
|
+
end
|
|
84
|
+
|
|
85
|
+
def output_data(input)
|
|
86
|
+
# Pass the input to subsequent pipelines
|
|
87
|
+
case options[:pass]
|
|
88
|
+
when IO
|
|
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|
+
options[:pass].print(input)
|
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|
+
else
|
|
91
|
+
if options[:pass]
|
|
92
|
+
File.open(options[:pass], 'w') do |f|
|
|
93
|
+
f.print(input)
|
|
92
94
|
end
|
|
93
95
|
end
|
|
96
|
+
end
|
|
97
|
+
end
|
|
94
98
|
|
|
99
|
+
def output_plot(plot)
|
|
100
|
+
case options[:output]
|
|
101
|
+
when IO
|
|
102
|
+
plot.render(options[:output])
|
|
103
|
+
else
|
|
104
|
+
File.open(options[:output], 'w') do |f|
|
|
105
|
+
plot.render(f)
|
|
106
|
+
end
|
|
95
107
|
end
|
|
96
108
|
end
|
|
97
109
|
end
|
|
@@ -1,28 +1,30 @@
|
|
|
1
1
|
# frozen_string_literal: true
|
|
2
2
|
|
|
3
3
|
require 'optparse'
|
|
4
|
-
require_relative '
|
|
4
|
+
require_relative 'cmd_options'
|
|
5
|
+
require_relative 'plot_params'
|
|
5
6
|
|
|
6
7
|
module YouPlot
|
|
7
8
|
class Command
|
|
8
9
|
class Parser
|
|
9
|
-
attr_reader :command, :params
|
|
10
|
-
:delimiter, :transpose, :headers, :pass, :output, :fmt,
|
|
11
|
-
:color_names, :encoding, :debug
|
|
10
|
+
attr_reader :command, :options, :params
|
|
12
11
|
|
|
13
12
|
def initialize
|
|
14
|
-
@command
|
|
15
|
-
@params = Params.new
|
|
13
|
+
@command = nil
|
|
16
14
|
|
|
17
|
-
@
|
|
18
|
-
|
|
19
|
-
|
|
20
|
-
|
|
21
|
-
|
|
22
|
-
|
|
23
|
-
|
|
24
|
-
|
|
25
|
-
|
|
15
|
+
@options = CmdOptions.new(
|
|
16
|
+
delimiter: "\t",
|
|
17
|
+
transpose: false,
|
|
18
|
+
headers: nil,
|
|
19
|
+
pass: false,
|
|
20
|
+
output: $stderr,
|
|
21
|
+
fmt: 'xyy',
|
|
22
|
+
encoding: nil,
|
|
23
|
+
color_names: false,
|
|
24
|
+
debug: false
|
|
25
|
+
)
|
|
26
|
+
|
|
27
|
+
@params = PlotParams.new
|
|
26
28
|
end
|
|
27
29
|
|
|
28
30
|
def create_default_parser
|
|
@@ -33,21 +35,22 @@ module YouPlot
|
|
|
33
35
|
opt.on_tail('') # Add a blank line at the end
|
|
34
36
|
opt.separator('')
|
|
35
37
|
opt.on('Common options:')
|
|
36
|
-
opt.on('-O', '--pass [
|
|
38
|
+
opt.on('-O', '--pass [FILE]', 'file to output input data to [stdout]',
|
|
37
39
|
'for inserting YouPlot in the middle of Unix pipes') do |v|
|
|
38
|
-
@pass = v || $stdout
|
|
40
|
+
@options[:pass] = v || $stdout
|
|
39
41
|
end
|
|
40
|
-
opt.on('-o', '--output
|
|
41
|
-
|
|
42
|
+
opt.on('-o', '--output [FILE]', 'file to output plots to [stdout]',
|
|
43
|
+
'If no option is specified, plot will print to stderr') do |v|
|
|
44
|
+
@options[:output] = v || $stdout
|
|
42
45
|
end
|
|
43
46
|
opt.on('-d', '--delimiter VAL', String, 'use DELIM instead of TAB for field delimiter') do |v|
|
|
44
|
-
@delimiter = v
|
|
47
|
+
@options[:delimiter] = v
|
|
45
48
|
end
|
|
46
49
|
opt.on('-H', '--headers', TrueClass, 'specify that the input has header row') do |v|
|
|
47
|
-
@headers = v
|
|
50
|
+
@options[:headers] = v
|
|
48
51
|
end
|
|
49
52
|
opt.on('-T', '--transpose', TrueClass, 'transpose the axes of the input data') do |v|
|
|
50
|
-
@transpose = v
|
|
53
|
+
@options[:transpose] = v
|
|
51
54
|
end
|
|
52
55
|
opt.on('-t', '--title VAL', String, 'print string on the top of plot') do |v|
|
|
53
56
|
params.title = v
|
|
@@ -79,8 +82,11 @@ module YouPlot
|
|
|
79
82
|
opt.on('--[no-]labels', TrueClass, 'hide the labels') do |v|
|
|
80
83
|
params.labels = v
|
|
81
84
|
end
|
|
85
|
+
opt.on('--progress', TrueClass, 'progressive') do |v|
|
|
86
|
+
@options[:progressive] = v
|
|
87
|
+
end
|
|
82
88
|
opt.on('--encoding VAL', String, 'Specify the input encoding') do |v|
|
|
83
|
-
@encoding = v
|
|
89
|
+
@options[:encoding] = v
|
|
84
90
|
end
|
|
85
91
|
# Optparse adds the help option, but it doesn't show up in usage.
|
|
86
92
|
# This is why you need the code below.
|
|
@@ -89,7 +95,7 @@ module YouPlot
|
|
|
89
95
|
exit
|
|
90
96
|
end
|
|
91
97
|
opt.on('--debug', TrueClass, 'print preprocessed data') do |v|
|
|
92
|
-
@debug = v
|
|
98
|
+
@options[:debug] = v
|
|
93
99
|
end
|
|
94
100
|
yield opt if block_given?
|
|
95
101
|
end
|
|
@@ -117,7 +123,7 @@ module YouPlot
|
|
|
117
123
|
scatter s draw a scatter plot
|
|
118
124
|
density d draw a density plot
|
|
119
125
|
boxplot box draw a horizontal boxplot
|
|
120
|
-
colors
|
|
126
|
+
colors color show the list of available colors
|
|
121
127
|
|
|
122
128
|
count c draw a baplot based on the number of
|
|
123
129
|
occurrences (slow)
|
|
@@ -163,7 +169,7 @@ module YouPlot
|
|
|
163
169
|
params.xscale = v
|
|
164
170
|
end
|
|
165
171
|
parser.on_head('--fmt VAL', String, 'xy : header is like x, y...', 'yx : header is like y, x...') do |v|
|
|
166
|
-
@fmt = v
|
|
172
|
+
@options[:fmt] = v
|
|
167
173
|
end
|
|
168
174
|
|
|
169
175
|
when :count, :c
|
|
@@ -193,7 +199,7 @@ module YouPlot
|
|
|
193
199
|
params.ylim = v.take(2)
|
|
194
200
|
end
|
|
195
201
|
parser.on_head('--fmt VAL', String, 'xy : header is like x, y...', 'yx : header is like y, x...') do |v|
|
|
196
|
-
@fmt = v
|
|
202
|
+
@options[:fmt] = v
|
|
197
203
|
end
|
|
198
204
|
|
|
199
205
|
when :lineplots, :lines
|
|
@@ -206,8 +212,9 @@ module YouPlot
|
|
|
206
212
|
parser.on_head('--ylim VAL', Array, 'plotting range for the y coordinate') do |v|
|
|
207
213
|
params.ylim = v.take(2)
|
|
208
214
|
end
|
|
209
|
-
parser.on_head('--fmt VAL', String, 'xyxy : header is like x1, y1, x2, y2, x3, y3...',
|
|
210
|
-
|
|
215
|
+
parser.on_head('--fmt VAL', String, 'xyxy : header is like x1, y1, x2, y2, x3, y3...',
|
|
216
|
+
'xyy : header is like x, y1, y2, y2, y3...') do |v|
|
|
217
|
+
@options[:fmt] = v
|
|
211
218
|
end
|
|
212
219
|
|
|
213
220
|
when :scatter, :s
|
|
@@ -220,8 +227,9 @@ module YouPlot
|
|
|
220
227
|
parser.on_head('--ylim VAL', Array, 'plotting range for the y coordinate') do |v|
|
|
221
228
|
params.ylim = v.take(2)
|
|
222
229
|
end
|
|
223
|
-
parser.on_head('--fmt VAL', String, 'xyxy : header is like x1, y1, x2, y2, x3, y3...',
|
|
224
|
-
|
|
230
|
+
parser.on_head('--fmt VAL', String, 'xyxy : header is like x1, y1, x2, y2, x3, y3...',
|
|
231
|
+
'xyy : header is like x, y1, y2, y2, y3...') do |v|
|
|
232
|
+
@options[:fmt] = v
|
|
225
233
|
end
|
|
226
234
|
|
|
227
235
|
when :density, :d
|
|
@@ -234,8 +242,9 @@ module YouPlot
|
|
|
234
242
|
parser.on_head('--ylim VAL', Array, 'plotting range for the y coordinate') do |v|
|
|
235
243
|
params.ylim = v.take(2)
|
|
236
244
|
end
|
|
237
|
-
parser.on('--fmt VAL', String, 'xyxy : header is like x1, y1, x2, y2, x3, y3...',
|
|
238
|
-
|
|
245
|
+
parser.on('--fmt VAL', String, 'xyxy : header is like x1, y1, x2, y2, x3, y3...',
|
|
246
|
+
'xyy : header is like x, y1, y2, y2, y3...') do |v|
|
|
247
|
+
@options[:fmt] = v
|
|
239
248
|
end
|
|
240
249
|
|
|
241
250
|
when :boxplot, :box
|
|
@@ -243,9 +252,9 @@ module YouPlot
|
|
|
243
252
|
params.xlim = v.take(2)
|
|
244
253
|
end
|
|
245
254
|
|
|
246
|
-
when :colors
|
|
255
|
+
when :colors, :color, :colours, :colour
|
|
247
256
|
parser.on_head('-n', '--names', 'show color names only', TrueClass) do |v|
|
|
248
|
-
@color_names = v
|
|
257
|
+
@options[:color_names] = v
|
|
249
258
|
end
|
|
250
259
|
|
|
251
260
|
else
|
data/lib/youplot/version.rb
CHANGED
metadata
CHANGED
|
@@ -1,14 +1,14 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: youplot
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 0.3.
|
|
4
|
+
version: 0.3.2
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- kojix2
|
|
8
8
|
autorequire:
|
|
9
9
|
bindir: exe
|
|
10
10
|
cert_chain: []
|
|
11
|
-
date: 2020-12-
|
|
11
|
+
date: 2020-12-17 00:00:00.000000000 Z
|
|
12
12
|
dependencies:
|
|
13
13
|
- !ruby/object:Gem::Dependency
|
|
14
14
|
name: unicode_plot
|
|
@@ -112,8 +112,9 @@ files:
|
|
|
112
112
|
- lib/youplot/backends/processing.rb
|
|
113
113
|
- lib/youplot/backends/unicode_plot_backend.rb
|
|
114
114
|
- lib/youplot/command.rb
|
|
115
|
-
- lib/youplot/command/
|
|
115
|
+
- lib/youplot/command/cmd_options.rb
|
|
116
116
|
- lib/youplot/command/parser.rb
|
|
117
|
+
- lib/youplot/command/plot_params.rb
|
|
117
118
|
- lib/youplot/dsv_reader.rb
|
|
118
119
|
- lib/youplot/version.rb
|
|
119
120
|
homepage: https://github.com/kojix2/youplot
|