youplot 0.3.1 → 0.4.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/README.md +177 -67
- data/exe/uplot +1 -1
- data/exe/youplot +1 -1
- data/lib/youplot.rb +12 -4
- data/lib/youplot/backends/processing.rb +11 -7
- data/lib/youplot/backends/{unicode_plot_backend.rb → unicode_plot.rb} +53 -34
- data/lib/youplot/command.rb +189 -70
- data/lib/youplot/dsv.rb +87 -0
- data/lib/youplot/options.rb +18 -0
- data/lib/youplot/parameters.rb +34 -0
- data/lib/youplot/parser.rb +306 -0
- data/lib/youplot/version.rb +1 -1
- metadata +10 -10
- data/lib/youplot/command/params.rb +0 -37
- data/lib/youplot/command/parser.rb +0 -277
- data/lib/youplot/dsv_reader.rb +0 -73
checksums.yaml
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data/README.md
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<p align="center">
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<img src="logo.svg" width="60%" height="60%" />
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</p>
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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]` or
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* `uplot <command> [options] <data.tsv>`
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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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<
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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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### histogram
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```sh
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echo -e "from numpy import random;" \
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| uplot hist --nbins 20
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```
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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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### lineplot
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```sh
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curl -
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| uplot
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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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<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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### scatter
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```sh
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curl -
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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 scatter -H -t IRIS
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```
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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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### density
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```sh
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curl -
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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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<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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### 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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<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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### 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 it creates 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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Program: YouPlot (Tools for plotting on the terminal)
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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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<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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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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Note: `count` is not very fast because it runs in a Ruby script.
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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.
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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 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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| Command | Description |
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|------------------------------------------------|-----------------------------------|
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| `cat data.tsv \| uplot <command> [options]` | Take input from stdin |
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| `uplot <command> [options] data.tsv ...` | Take input from files |
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| `pipeline1 \| uplot <command> -O \| pipeline2` | Outputs data from stdin to stdout |
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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 shown anywhere.
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The `-O` option, with no arguments, outputs the input data directly to the standard output.
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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 barplot based on the number of occurrences (slow) |
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### What if the header line is included?
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If your input data contains a header line, you need to specify the `-H` option.
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### How to specify the delimiter?
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Use the `-d` option. To specify a blank space, you can use `uplot bar -d ' ' data.txt`.
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You do not need to use `-d` option for tab-delimited text since the default value is tab.
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### Is there a way to specify a column as the x-axis or y-axis?
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Not yet.
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YouPlot treats the first column as the X axis and the second column as the Y axis.
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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.
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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.
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* `--fmt xyy` `--fmt xyxy` `--fmt yx` options give you a few more choices.
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See `youplot <command> --help` for more details.
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* Use `awk '{print $2, $1}'` to swap lines.
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* Use `paste` to concatenate series.
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### How to plot real-time data?
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Experimental progressive mode is currently under development.
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```sh
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ruby -e 'loop{puts rand(100)}' | uplot line --progress
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```
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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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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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--closed VAL side of the intervals to be closed [left]
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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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YouPlot is a library under development, so even small improvements like typofix are welcome!
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Please feel free to send us your pull requests.
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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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* English corrections by native speakers are welcome.
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* Suggest or add new features
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* Make a donation
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### Development
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```sh
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# fork the main repository by clicking the Fork button.
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git clone https://github.com/your_name/YouPlot
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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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### Acknowledgements
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|
+
|
|
252
|
+
* [Red Data Tools](https://github.com/red-data-tools) - Technical support
|
|
253
|
+
* [sampo grafiikka](https://jypg.net/sampo_grafiikka) - Project logo creation
|
|
254
|
+
* [yutaas](https://github.com/yutaas) - English proofreading
|
|
145
255
|
|
|
146
256
|
## License
|
|
147
257
|
|
data/exe/uplot
CHANGED
data/exe/youplot
CHANGED
data/lib/youplot.rb
CHANGED
|
@@ -1,9 +1,17 @@
|
|
|
1
1
|
# frozen_string_literal: true
|
|
2
2
|
|
|
3
|
-
|
|
4
|
-
|
|
5
|
-
|
|
6
|
-
|
|
3
|
+
require_relative 'youplot/version'
|
|
4
|
+
require_relative 'youplot/dsv'
|
|
5
|
+
require_relative 'youplot/parameters'
|
|
6
|
+
require_relative 'youplot/command'
|
|
7
7
|
|
|
8
8
|
module YouPlot
|
|
9
|
+
class << self
|
|
10
|
+
attr_accessor :run_as_executable
|
|
11
|
+
|
|
12
|
+
def run_as_executable?
|
|
13
|
+
@run_as_executable
|
|
14
|
+
end
|
|
15
|
+
end
|
|
16
|
+
@run_as_executable = false
|
|
9
17
|
end
|
|
@@ -6,17 +6,21 @@ module YouPlot
|
|
|
6
6
|
module Processing
|
|
7
7
|
module_function
|
|
8
8
|
|
|
9
|
-
def count_values(arr)
|
|
9
|
+
def count_values(arr, tally: true)
|
|
10
10
|
# tally was added in Ruby 2.7
|
|
11
|
-
if Enumerable.method_defined?
|
|
11
|
+
if tally && Enumerable.method_defined?(:tally)
|
|
12
12
|
arr.tally
|
|
13
13
|
else
|
|
14
|
-
#
|
|
15
|
-
arr.
|
|
16
|
-
.tap { |h| h.default = nil }
|
|
14
|
+
# value_counts Enumerable::Statistics
|
|
15
|
+
arr.value_counts(dropna: false)
|
|
17
16
|
end
|
|
18
|
-
.sort
|
|
19
|
-
|
|
17
|
+
.sort do |a, b|
|
|
18
|
+
# compare values
|
|
19
|
+
r = b[1] <=> a[1]
|
|
20
|
+
# If the values are the same, compare by name
|
|
21
|
+
r = a[0] <=> b[0] if r == 0
|
|
22
|
+
r
|
|
23
|
+
end
|
|
20
24
|
.transpose
|
|
21
25
|
end
|
|
22
26
|
end
|
|
@@ -1,12 +1,17 @@
|
|
|
1
1
|
# frozen_string_literal: true
|
|
2
2
|
|
|
3
|
+
# UnicodePlot - Plot your data by Unicode characters
|
|
4
|
+
# https://github.com/red-data-tools/unicode_plot.rb
|
|
5
|
+
|
|
3
6
|
require_relative 'processing'
|
|
4
7
|
require 'unicode_plot'
|
|
5
8
|
|
|
6
9
|
module YouPlot
|
|
7
10
|
# plotting functions.
|
|
8
11
|
module Backends
|
|
9
|
-
module
|
|
12
|
+
module UnicodePlot
|
|
13
|
+
class Error < StandardError; end
|
|
14
|
+
|
|
10
15
|
module_function
|
|
11
16
|
|
|
12
17
|
def barplot(data, params, fmt = nil, count: false)
|
|
@@ -37,7 +42,7 @@ module YouPlot
|
|
|
37
42
|
labels = series[x_col]
|
|
38
43
|
values = series[y_col].map(&:to_f)
|
|
39
44
|
end
|
|
40
|
-
UnicodePlot.barplot(labels, values, **params.to_hc)
|
|
45
|
+
::UnicodePlot.barplot(labels, values, **params.to_hc)
|
|
41
46
|
end
|
|
42
47
|
|
|
43
48
|
def histogram(data, params)
|
|
@@ -45,7 +50,7 @@ module YouPlot
|
|
|
45
50
|
series = data.series
|
|
46
51
|
params.title ||= data.headers[0] if headers
|
|
47
52
|
values = series[0].map(&:to_f)
|
|
48
|
-
UnicodePlot.histogram(values, **params.to_hc)
|
|
53
|
+
::UnicodePlot.histogram(values, **params.to_hc)
|
|
49
54
|
end
|
|
50
55
|
|
|
51
56
|
def line(data, params, fmt = nil)
|
|
@@ -55,7 +60,7 @@ module YouPlot
|
|
|
55
60
|
# If there is only one series, it is assumed to be sequential data.
|
|
56
61
|
params.ylabel ||= headers[0] if headers
|
|
57
62
|
y = series[0].map(&:to_f)
|
|
58
|
-
UnicodePlot.lineplot(y, **params.to_hc)
|
|
63
|
+
::UnicodePlot.lineplot(y, **params.to_hc)
|
|
59
64
|
else
|
|
60
65
|
# If there are 2 or more series...
|
|
61
66
|
if fmt == 'yx'
|
|
@@ -73,7 +78,7 @@ module YouPlot
|
|
|
73
78
|
end
|
|
74
79
|
x = series[x_col].map(&:to_f)
|
|
75
80
|
y = series[y_col].map(&:to_f)
|
|
76
|
-
UnicodePlot.lineplot(x, y, **params.to_hc)
|
|
81
|
+
::UnicodePlot.lineplot(x, y, **params.to_hc)
|
|
77
82
|
end
|
|
78
83
|
end
|
|
79
84
|
|
|
@@ -90,10 +95,11 @@ module YouPlot
|
|
|
90
95
|
params.name ||= headers[1]
|
|
91
96
|
params.xlabel ||= headers[0]
|
|
92
97
|
end
|
|
98
|
+
params.xlim ||= series[0].flatten.minmax # why need?
|
|
93
99
|
params.ylim ||= series[1..-1].flatten.minmax # why need?
|
|
94
|
-
plot = UnicodePlot.public_send(method1, series[0], series[1], **params.to_hc)
|
|
100
|
+
plot = ::UnicodePlot.public_send(method1, series[0], series[1], **params.to_hc)
|
|
95
101
|
2.upto(series.size - 1) do |i|
|
|
96
|
-
UnicodePlot.public_send(method2, plot, series[0], series[i], name: headers&.[](i))
|
|
102
|
+
::UnicodePlot.public_send(method2, plot, series[0], series[i], name: headers&.[](i))
|
|
97
103
|
end
|
|
98
104
|
plot
|
|
99
105
|
end
|
|
@@ -103,14 +109,15 @@ module YouPlot
|
|
|
103
109
|
series = data.series
|
|
104
110
|
method2 = get_method2(method1)
|
|
105
111
|
series.map! { |s| s.map(&:to_f) }
|
|
106
|
-
|
|
112
|
+
series2 = series.each_slice(2).to_a
|
|
113
|
+
series = nil
|
|
107
114
|
params.name ||= headers[0] if headers
|
|
108
|
-
params.xlim
|
|
109
|
-
params.ylim
|
|
110
|
-
x1, y1 =
|
|
111
|
-
plot = UnicodePlot.public_send(method1, x1, y1, **params.to_hc)
|
|
112
|
-
|
|
113
|
-
UnicodePlot.public_send(method2, plot, xi, yi, name: headers&.[]((i + 1) * 2))
|
|
115
|
+
params.xlim ||= series2.map(&:first).flatten.minmax # why need?
|
|
116
|
+
params.ylim ||= series2.map(&:last).flatten.minmax # why need?
|
|
117
|
+
x1, y1 = series2.shift
|
|
118
|
+
plot = ::UnicodePlot.public_send(method1, x1, y1, **params.to_hc)
|
|
119
|
+
series2.each_with_index do |(xi, yi), i|
|
|
120
|
+
::UnicodePlot.public_send(method2, plot, xi, yi, name: headers&.[]((i + 1) * 2))
|
|
114
121
|
end
|
|
115
122
|
plot
|
|
116
123
|
end
|
|
@@ -148,39 +155,51 @@ module YouPlot
|
|
|
148
155
|
series = data.series
|
|
149
156
|
headers ||= (1..series.size).map(&:to_s)
|
|
150
157
|
series.map! { |s| s.map(&:to_f) }
|
|
151
|
-
UnicodePlot.boxplot(headers, series, **params.to_hc)
|
|
158
|
+
::UnicodePlot.boxplot(headers, series, **params.to_hc)
|
|
152
159
|
end
|
|
153
160
|
|
|
154
161
|
def colors(color_names = false)
|
|
155
|
-
|
|
156
|
-
|
|
157
|
-
|
|
162
|
+
# FIXME
|
|
163
|
+
s = String.new
|
|
164
|
+
::UnicodePlot::StyledPrinter::TEXT_COLORS.each do |k, v|
|
|
165
|
+
s << v
|
|
166
|
+
s << k.to_s
|
|
158
167
|
unless color_names
|
|
159
|
-
|
|
160
|
-
|
|
168
|
+
s << "\t"
|
|
169
|
+
s << ' ●'
|
|
161
170
|
end
|
|
162
|
-
|
|
163
|
-
|
|
171
|
+
s << "\033[0m"
|
|
172
|
+
s << "\t"
|
|
173
|
+
end
|
|
174
|
+
s << "\n"
|
|
175
|
+
def s.render(obj)
|
|
176
|
+
obj.print(self)
|
|
164
177
|
end
|
|
165
|
-
|
|
178
|
+
s
|
|
166
179
|
end
|
|
167
180
|
|
|
168
181
|
def check_series_size(data, fmt)
|
|
169
182
|
series = data.series
|
|
170
183
|
if series.size == 1
|
|
171
|
-
warn
|
|
172
|
-
|
|
173
|
-
|
|
174
|
-
|
|
175
|
-
|
|
176
|
-
|
|
184
|
+
warn <<~EOS
|
|
185
|
+
youplot: There is only one series of input data. Please check the delimiter.
|
|
186
|
+
|
|
187
|
+
Headers: \e[35m#{data.headers.inspect}\e[0m
|
|
188
|
+
The first item is: \e[35m\"#{series[0][0]}\"\e[0m
|
|
189
|
+
The last item is : \e[35m\"#{series[0][-1]}\"\e[0m
|
|
190
|
+
EOS
|
|
191
|
+
# NOTE: Error messages cannot be colored.
|
|
192
|
+
YouPlot.run_as_executable ? exit(1) : raise(Error)
|
|
177
193
|
end
|
|
178
194
|
if fmt == 'xyxy' && series.size.odd?
|
|
179
|
-
warn
|
|
180
|
-
|
|
181
|
-
|
|
182
|
-
|
|
183
|
-
|
|
195
|
+
warn <<~EOS
|
|
196
|
+
YouPlot: In the xyxy format, the number of series must be even.
|
|
197
|
+
|
|
198
|
+
Number of series: \e[35m#{series.size}\e[0m
|
|
199
|
+
Headers: \e[35m#{data.headers.inspect}\e[0m
|
|
200
|
+
EOS
|
|
201
|
+
# NOTE: Error messages cannot be colored.
|
|
202
|
+
YouPlot.run_as_executable ? exit(1) : raise(Error)
|
|
184
203
|
end
|
|
185
204
|
end
|
|
186
205
|
end
|