youplot 0.3.0 → 0.3.5
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- checksums.yaml +4 -4
- data/README.md +165 -67
- data/exe/uplot +1 -1
- data/exe/youplot +1 -1
- data/lib/youplot.rb +9 -1
- data/lib/youplot/backends/processing.rb +24 -0
- data/lib/youplot/backends/unicode_plot_backend.rb +73 -36
- data/lib/youplot/command.rb +152 -58
- data/lib/youplot/command/options.rb +19 -0
- data/lib/youplot/command/parser.rb +227 -183
- data/lib/youplot/command/{params.rb → plot_params.rb} +1 -1
- data/lib/youplot/{preprocessing.rb → dsv.rb} +15 -24
- data/lib/youplot/version.rb +1 -1
- metadata +9 -8
checksums.yaml
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<p align="center">
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<img src="logo.svg" width="60%" height="60%" />
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</7>
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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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| cut -
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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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| 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 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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| cut -f1-4
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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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| | |
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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 shown 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 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`. 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. In principle, YouPlot treats the first column as the X axis and the second column as the Y axis. When working with multiple series, the first row is the X axis, the second row is series 1, the third row is series 2, and so on. If you pass only one column of data for `line` and `bar`, YouPlot will automatically use a sequential number starting from 1 as the X-axis. The `--fmt xyy`, `--fmt xyxy` and `--fmt yx` options give you a few more choices. See `youplot <command> --help` for more details. YouPlot has limited functionalities, but you can use shell scripts such as `awk '{print $2, $1}'` to swap lines.
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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! 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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### 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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* [Red Data Tools](https://github.com/red-data-tools) - Technical support
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* [sampo grafiikka](https://jypg.net/sampo_grafiikka) - Project logo creation
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* [yutaas](https://github.com/yutaas) - English proofreading
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## License
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data/exe/uplot
CHANGED
data/exe/youplot
CHANGED
data/lib/youplot.rb
CHANGED
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@@ -2,8 +2,16 @@
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2
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3
3
|
require 'unicode_plot'
|
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4
4
|
require 'youplot/version'
|
|
5
|
-
require 'youplot/
|
|
5
|
+
require 'youplot/dsv'
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6
6
|
require 'youplot/command'
|
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7
7
|
|
|
8
8
|
module YouPlot
|
|
9
|
+
class << self
|
|
10
|
+
attr_accessor :run_as_executable
|
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11
|
+
|
|
12
|
+
def run_as_executable?
|
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13
|
+
@run_as_executable
|
|
14
|
+
end
|
|
15
|
+
end
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16
|
+
@run_as_executable = false
|
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9
17
|
end
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|
@@ -0,0 +1,24 @@
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|
1
|
+
# frozen_string_literal: true
|
|
2
|
+
|
|
3
|
+
module YouPlot
|
|
4
|
+
# plotting functions.
|
|
5
|
+
module Backends
|
|
6
|
+
module Processing
|
|
7
|
+
module_function
|
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8
|
+
|
|
9
|
+
def count_values(arr, tally: true)
|
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10
|
+
# tally was added in Ruby 2.7
|
|
11
|
+
if tally && Enumerable.method_defined?(:tally)
|
|
12
|
+
arr.tally
|
|
13
|
+
else
|
|
14
|
+
# https://github.com/marcandre/backports
|
|
15
|
+
arr.each_with_object(Hash.new(0)) { |item, res| res[item] += 1 }
|
|
16
|
+
.tap { |h| h.default = nil }
|
|
17
|
+
end
|
|
18
|
+
.sort { |a, b| a[1] <=> b[1] }
|
|
19
|
+
.reverse
|
|
20
|
+
.transpose
|
|
21
|
+
end
|
|
22
|
+
end
|
|
23
|
+
end
|
|
24
|
+
end
|
|
@@ -1,30 +1,43 @@
|
|
|
1
1
|
# frozen_string_literal: true
|
|
2
2
|
|
|
3
|
+
require_relative 'processing'
|
|
3
4
|
require 'unicode_plot'
|
|
4
5
|
|
|
5
6
|
module YouPlot
|
|
6
7
|
# plotting functions.
|
|
7
8
|
module Backends
|
|
8
9
|
module UnicodePlotBackend
|
|
10
|
+
class Error < StandardError; end
|
|
11
|
+
|
|
9
12
|
module_function
|
|
10
13
|
|
|
11
|
-
def barplot(data, params, count: false)
|
|
14
|
+
def barplot(data, params, fmt = nil, count: false)
|
|
12
15
|
headers = data.headers
|
|
13
16
|
series = data.series
|
|
14
17
|
# `uplot count`
|
|
15
18
|
if count
|
|
16
|
-
series =
|
|
19
|
+
series = Processing.count_values(series[0])
|
|
17
20
|
params.title = headers[0] if headers
|
|
18
21
|
end
|
|
19
22
|
if series.size == 1
|
|
20
|
-
# If there is only one series
|
|
23
|
+
# If there is only one series.use the line number for label.
|
|
21
24
|
params.title ||= headers[0] if headers
|
|
22
25
|
labels = Array.new(series[0].size) { |i| (i + 1).to_s }
|
|
23
26
|
values = series[0].map(&:to_f)
|
|
24
27
|
else
|
|
25
|
-
|
|
26
|
-
|
|
27
|
-
|
|
28
|
+
# If there are 2 or more series...
|
|
29
|
+
if fmt == 'yx'
|
|
30
|
+
# assume that the first 2 series are the y and x series respectively.
|
|
31
|
+
x_col = 1
|
|
32
|
+
y_col = 0
|
|
33
|
+
else
|
|
34
|
+
# assume that the first 2 series are the x and y series respectively.
|
|
35
|
+
x_col = 0
|
|
36
|
+
y_col = 1
|
|
37
|
+
end
|
|
38
|
+
params.title ||= headers[y_col] if headers
|
|
39
|
+
labels = series[x_col]
|
|
40
|
+
values = series[y_col].map(&:to_f)
|
|
28
41
|
end
|
|
29
42
|
UnicodePlot.barplot(labels, values, **params.to_hc)
|
|
30
43
|
end
|
|
@@ -37,7 +50,7 @@ module YouPlot
|
|
|
37
50
|
UnicodePlot.histogram(values, **params.to_hc)
|
|
38
51
|
end
|
|
39
52
|
|
|
40
|
-
def line(data, params)
|
|
53
|
+
def line(data, params, fmt = nil)
|
|
41
54
|
headers = data.headers
|
|
42
55
|
series = data.series
|
|
43
56
|
if series.size == 1
|
|
@@ -46,14 +59,22 @@ module YouPlot
|
|
|
46
59
|
y = series[0].map(&:to_f)
|
|
47
60
|
UnicodePlot.lineplot(y, **params.to_hc)
|
|
48
61
|
else
|
|
49
|
-
# If there are 2 or more series
|
|
50
|
-
|
|
62
|
+
# If there are 2 or more series...
|
|
63
|
+
if fmt == 'yx'
|
|
64
|
+
# assume that the first 2 series are the y and x series respectively.
|
|
65
|
+
x_col = 1
|
|
66
|
+
y_col = 0
|
|
67
|
+
else
|
|
68
|
+
# assume that the first 2 series are the x and y series respectively.
|
|
69
|
+
x_col = 0
|
|
70
|
+
y_col = 1
|
|
71
|
+
end
|
|
51
72
|
if headers
|
|
52
|
-
params.xlabel ||= headers[
|
|
53
|
-
params.ylabel ||= headers[
|
|
73
|
+
params.xlabel ||= headers[x_col]
|
|
74
|
+
params.ylabel ||= headers[y_col]
|
|
54
75
|
end
|
|
55
|
-
x = series[
|
|
56
|
-
y = series[
|
|
76
|
+
x = series[x_col].map(&:to_f)
|
|
77
|
+
y = series[y_col].map(&:to_f)
|
|
57
78
|
UnicodePlot.lineplot(x, y, **params.to_hc)
|
|
58
79
|
end
|
|
59
80
|
end
|
|
@@ -71,6 +92,7 @@ module YouPlot
|
|
|
71
92
|
params.name ||= headers[1]
|
|
72
93
|
params.xlabel ||= headers[0]
|
|
73
94
|
end
|
|
95
|
+
params.xlim ||= series[0].flatten.minmax # why need?
|
|
74
96
|
params.ylim ||= series[1..-1].flatten.minmax # why need?
|
|
75
97
|
plot = UnicodePlot.public_send(method1, series[0], series[1], **params.to_hc)
|
|
76
98
|
2.upto(series.size - 1) do |i|
|
|
@@ -84,13 +106,14 @@ module YouPlot
|
|
|
84
106
|
series = data.series
|
|
85
107
|
method2 = get_method2(method1)
|
|
86
108
|
series.map! { |s| s.map(&:to_f) }
|
|
87
|
-
|
|
109
|
+
series2 = series.each_slice(2).to_a
|
|
110
|
+
series = nil
|
|
88
111
|
params.name ||= headers[0] if headers
|
|
89
|
-
params.xlim
|
|
90
|
-
params.ylim
|
|
91
|
-
x1, y1 =
|
|
112
|
+
params.xlim ||= series2.map(&:first).flatten.minmax # why need?
|
|
113
|
+
params.ylim ||= series2.map(&:last).flatten.minmax # why need?
|
|
114
|
+
x1, y1 = series2.shift
|
|
92
115
|
plot = UnicodePlot.public_send(method1, x1, y1, **params.to_hc)
|
|
93
|
-
|
|
116
|
+
series2.each_with_index do |(xi, yi), i|
|
|
94
117
|
UnicodePlot.public_send(method2, plot, xi, yi, name: headers&.[]((i + 1) * 2))
|
|
95
118
|
end
|
|
96
119
|
plot
|
|
@@ -102,6 +125,8 @@ module YouPlot
|
|
|
102
125
|
plot_xyy(data, method1, params)
|
|
103
126
|
when 'xyxy'
|
|
104
127
|
plot_xyxy(data, method1, params)
|
|
128
|
+
when 'yx'
|
|
129
|
+
raise "Incorrect format: #{fmt}"
|
|
105
130
|
else
|
|
106
131
|
raise "Unknown format: #{fmt}"
|
|
107
132
|
end
|
|
@@ -131,35 +156,47 @@ module YouPlot
|
|
|
131
156
|
end
|
|
132
157
|
|
|
133
158
|
def colors(color_names = false)
|
|
159
|
+
# FIXME
|
|
160
|
+
s = String.new
|
|
134
161
|
UnicodePlot::StyledPrinter::TEXT_COLORS.each do |k, v|
|
|
135
|
-
|
|
136
|
-
|
|
162
|
+
s << v
|
|
163
|
+
s << k.to_s
|
|
137
164
|
unless color_names
|
|
138
|
-
|
|
139
|
-
|
|
165
|
+
s << "\t"
|
|
166
|
+
s << ' ●'
|
|
140
167
|
end
|
|
141
|
-
|
|
142
|
-
|
|
168
|
+
s << "\033[0m"
|
|
169
|
+
s << "\t"
|
|
143
170
|
end
|
|
144
|
-
|
|
171
|
+
s << "\n"
|
|
172
|
+
def s.render(obj)
|
|
173
|
+
obj.print(self)
|
|
174
|
+
end
|
|
175
|
+
s
|
|
145
176
|
end
|
|
146
177
|
|
|
147
178
|
def check_series_size(data, fmt)
|
|
148
179
|
series = data.series
|
|
149
180
|
if series.size == 1
|
|
150
|
-
warn
|
|
151
|
-
|
|
152
|
-
|
|
153
|
-
|
|
154
|
-
|
|
155
|
-
|
|
181
|
+
warn <<~EOS
|
|
182
|
+
youplot: There is only one series of input data. Please check the delimiter.
|
|
183
|
+
|
|
184
|
+
Headers: \e[35m#{data.headers.inspect}\e[0m
|
|
185
|
+
The first item is: \e[35m\"#{series[0][0]}\"\e[0m
|
|
186
|
+
The last item is : \e[35m\"#{series[0][-1]}\"\e[0m
|
|
187
|
+
EOS
|
|
188
|
+
# NOTE: Error messages cannot be colored.
|
|
189
|
+
YouPlot.run_as_executable ? exit(1) : raise(Error)
|
|
156
190
|
end
|
|
157
191
|
if fmt == 'xyxy' && series.size.odd?
|
|
158
|
-
warn
|
|
159
|
-
|
|
160
|
-
|
|
161
|
-
|
|
162
|
-
|
|
192
|
+
warn <<~EOS
|
|
193
|
+
YouPlot: In the xyxy format, the number of series must be even.
|
|
194
|
+
|
|
195
|
+
Number of series: \e[35m#{series.size}\e[0m
|
|
196
|
+
Headers: \e[35m#{data.headers.inspect}\e[0m
|
|
197
|
+
EOS
|
|
198
|
+
# NOTE: Error messages cannot be colored.
|
|
199
|
+
YouPlot.run_as_executable ? exit(1) : raise(Error)
|
|
163
200
|
end
|
|
164
201
|
end
|
|
165
202
|
end
|