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							| @@ -3,11 +3,11 @@ | |||||||
|    |    | ||||||
|   <hr> |   <hr> | ||||||
|    |    | ||||||
|    |   <img alt="Build Status" src="https://github.com/red-data-tools/YouPlot/workflows/test/badge.svg"> | ||||||
|   [](https://badge.fury.io/rb/youplot) |   <a href="https://rubygems.org/gems/youplot/"><img alt="Gem Version" src="https://badge.fury.io/rb/youplot.svg"></a> | ||||||
|   [](https://rubydoc.info/gems/youplot) |   <a href="https://rubydoc.info/gems/youplot/"><img alt="Docs Stable" src="https://img.shields.io/badge/docs-stable-blue.svg"></a> | ||||||
|   [](LICENSE.txt) |   <a href="LICENSE.txt"><img alt="The MIT License" src="https://img.shields.io/badge/license-MIT-blue.svg"></a> | ||||||
|   [](https://zenodo.org/badge/latestdoi/283230219) |   <a href="https://zenodo.org/badge/latestdoi/283230219"><img alt="DOI" src="https://zenodo.org/badge/283230219.svg"></a> | ||||||
|    |    | ||||||
|   YouPlot is a command line tool that draws plots in the terminal. |   YouPlot is a command line tool that draws plots in the terminal. | ||||||
|  |  | ||||||
| @@ -126,12 +126,7 @@ cat gencode.v35.annotation.gff3 | grep -v '#' | grep 'gene' | cut -f1 \ | |||||||
|  |  | ||||||
| ## Usage | ## Usage | ||||||
|  |  | ||||||
| ### Why YouPlot? | ### Commands | ||||||
|  |  | ||||||
| Wouldn't it be a pain to have to run R, Python, Julia, gnuplot or whatever REPL just to check your data? |  | ||||||
| YouPlot is a command line tool for this purpose. With YouPlot, you can continue working without leaving your terminal and shell. |  | ||||||
|  |  | ||||||
| ### How to use YouPlot? |  | ||||||
|  |  | ||||||
| `uplot` is the shortened form of `youplot`. You can use either. | `uplot` is the shortened form of `youplot`. You can use either. | ||||||
|  |  | ||||||
| @@ -154,83 +149,65 @@ The following sub-commands are available. | |||||||
| | scatter   | s     | draw a scatter plot                    | | | scatter   | s     | draw a scatter plot                    | | ||||||
| | density   | d     | draw a density plot                    | | | density   | d     | draw a density plot                    | | ||||||
| | boxplot   | box   | draw a horizontal boxplot              | | | boxplot   | box   | draw a horizontal boxplot              | | ||||||
|  | |           |       |                                        | | ||||||
|  | | count     | c     | draw a barplot based on the number of occurrences (slow) | | ||||||
|  | |           |       |                                        | | ||||||
|  | | colors    | color | show the list of available colors      | | ||||||
|  |  | ||||||
| See Quick Start for `count`. | ### Output the plot | ||||||
|  |  | ||||||
| | command   | short | how it works                                             | | * `-o` | ||||||
| |-----------|-------|----------------------------------------------------------| |   * By default, the plot is output to **standard error output**. | ||||||
| | count     | c     |  draw a barplot based on the number of occurrences (slow) | |   * If you want to output to standard input, Use hyphen ` -o -` or no argument `uplot s -o | `. | ||||||
|  |  | ||||||
| ### Where to output the plot? | ### Output the input data | ||||||
|  |  | ||||||
| By default, the plot is output to *standard error output*. | * `-O` | ||||||
| The output file or stream for the plot can be specified with the `-o` option. |   * By default, the input data is not shown anywhere. | ||||||
|  |   * If you want to pass the input data directly to the standard output, Use hyphen `-O -` or no argument `uplot s -O |`. | ||||||
|  |   * This is useful when passing data to a subsequent pipeline. | ||||||
|  |  | ||||||
| ### Where to output the input data? | ### Header | ||||||
|  |  | ||||||
| By default, the input data is not shown anywhere. | * `-H` | ||||||
| The `-O` option, with no arguments, outputs the input data directly to the standard output.  |   * If input data contains a header line, you need to specify the `-H` option. | ||||||
| This is useful when passing data to a subsequent pipeline. |  | ||||||
|  |  | ||||||
| ### What if the header line is included? | ### Delimiter | ||||||
|  |  | ||||||
| If your input data contains a header line, you need to specify the `-H` option. | * `-d` | ||||||
|  |   * You do not need to use `-d` option for tab-delimited text since the default value is tab. | ||||||
|  |   * To specify a blank space, you can use `uplot bar -d ' ' data.txt`.  | ||||||
|  |  | ||||||
| ### How to specify the delimiter? | ### Real-time data | ||||||
|  |  | ||||||
| Use the `-d` option. To specify a blank space, you can use `uplot bar -d ' ' data.txt`.  | * `-p` `--progress` | ||||||
| You do not need to use `-d` option for tab-delimited text since the default value is tab. |   * Experimental progressive mode is currently under development. | ||||||
|  |   * `ruby -e 'loop{puts rand(100)}' | uplot line --progress` | ||||||
|  |  | ||||||
| ### Is there a way to specify a column as the x-axis or y-axis? | ### Show detailed options for subcommands | ||||||
|  |  | ||||||
| Not yet.  | * `--help` | ||||||
| YouPlot treats the first column as the X axis and the second column as the Y axis.  |   * The `--help` option will show more detailed options for each subcommand. | ||||||
| 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.  |   * `uplot hist --help` | ||||||
| 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.  |  | ||||||
|  |  | ||||||
| * `--fmt xyy` `--fmt xyxy` `--fmt yx` options give you a few more choices.  | ### Set columnss as x-axis or y-axis? | ||||||
| See `youplot <command> --help` for more details.  |  | ||||||
|  |  | ||||||
| * Use `awk '{print $2, $1}'` to swap lines. | * YouPlot treats the first column as the X axis and the second column as the Y axis. When working with multiple series, the first column is the X axis, the second column is series Y1, the third column is series Y2, and so on.  | ||||||
| * Use `paste` to concatenate series. | * 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.  | ||||||
|  |  | ||||||
| ### How to plot real-time data? | * `--fmt` | ||||||
|  |   * `--fmt xyy` `--fmt xyxy` `--fmt yx` options give you a few more choices. See `youplot <command> --help` for more details.  | ||||||
|  |   * The fmt option may be renamed in the future.  | ||||||
|  |   * The `-x` and `-y` options are currently used to specify labels `--xlabel` `--ylabel`, but may be used to specify columns in the future. | ||||||
|  |  | ||||||
| Experimental progressive mode is currently under development. | * Use `awk '{print $2, $1}'` to swap columns. Use `paste` to concatenate series. | ||||||
|  |  | ||||||
| ```sh | ## Tools that are useful to use with YouPlot | ||||||
| ruby -e 'loop{puts rand(100)}' | uplot line --progress |  | ||||||
| ``` |  | ||||||
|  |  | ||||||
| ### How to view detailed command line options? |  | ||||||
|  |  | ||||||
| Use `--help` to print command-specific options. |  | ||||||
|  |  | ||||||
| `uplot hist --help` |  | ||||||
|  |  | ||||||
| ``` |  | ||||||
| Usage: uplot histogram [options] <in.tsv> |  | ||||||
|  |  | ||||||
| Options for histogram: |  | ||||||
|         --symbol VAL         character to be used to plot the bars |  | ||||||
|         --closed VAL         side of the intervals to be closed [left] |  | ||||||
|     -n, --nbins VAL          approximate number of bins |  | ||||||
|  |  | ||||||
| Options: |  | ||||||
| ... |  | ||||||
| ``` |  | ||||||
|  |  | ||||||
| ### How to view the list of available colors? |  | ||||||
|  |  | ||||||
| ```sh |  | ||||||
| uplot colors |  | ||||||
| ``` |  | ||||||
|  |  | ||||||
| ## Command line tools that are useful to use with YouPlot |  | ||||||
|  |  | ||||||
| * [csvtk](https://github.com/shenwei356/csvtk) | * [csvtk](https://github.com/shenwei356/csvtk) | ||||||
| * [GNU datamash](https://www.gnu.org/software/datamash/) | * [GNU datamash](https://www.gnu.org/software/datamash/) | ||||||
| * [awk](https://www.gnu.org/software/gawk/) | * [awk](https://www.gnu.org/software/gawk/) | ||||||
|  | * [xsv](https://github.com/BurntSushi/xsv) | ||||||
|  |  | ||||||
| ## Contributing | ## Contributing | ||||||
|  |  | ||||||
| @@ -252,6 +229,7 @@ git clone https://github.com/your_name/YouPlot | |||||||
| bundle install             # Install the gem dependencies | bundle install             # Install the gem dependencies | ||||||
| bundle exec rake test      # Run the test | bundle exec rake test      # Run the test | ||||||
| bundle exec rake install   # Installation from source code | bundle exec rake install   # Installation from source code | ||||||
|  | bundle exec exe/uplot      # Run youplot (Try out the edited code) | ||||||
| ``` | ``` | ||||||
|  |  | ||||||
| ### Acknowledgements | ### Acknowledgements | ||||||
|   | |||||||
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