22 Commits

Author SHA1 Message Date
kojix2
e76d4f279e v0.4.3 2021-11-19 14:09:46 +09:00
kojix2
3a1a29424d Remove add_development_dependency from gem 2021-11-19 14:03:57 +09:00
kojix2
b78da2388a Rubocop auto correct 2021-11-19 13:56:09 +09:00
KIKISeries
a7bb75e87d Fix a typo
S -> s
2021-07-14 09:56:47 +09:00
kojix2
ca9f97a7dc Specify the version of UnicodePlot 2021-07-12 14:56:41 +09:00
kojix2
f67a5ce913 Add comments on the run_as_executable variable 2021-07-12 14:49:34 +09:00
kojix2
dbbfd366be Remove unused variable 2021-07-11 08:59:44 +09:00
kojix2
42cadee553 Improved CI
Remove needless line
2021-07-11 08:43:47 +09:00
kojix2
e689c69838 Update CI
* Enable bundler-cache
2021-07-11 08:38:05 +09:00
kojix2
c53169e9ee Update README.md (#24) 2021-07-03 07:22:19 +09:00
kojix2
95a35399a2 Show a error message when linecolor is specified as a number 2021-07-03 06:52:37 +09:00
kojix2
7c00f95962 Fix Readme style 2021-06-20 19:10:09 +09:00
kojix2
fcbf9305d7 Add StringIO for consistency 2021-06-18 10:43:28 +09:00
kojix2
04eddfd79b Fix typo 2021-06-17 08:19:04 +09:00
kojix2
125c2291d5 Add categorical/date to README 2021-06-17 08:13:58 +09:00
kojix2
6a72418d01 Update README 2021-06-17 07:49:51 +09:00
kojix2
72a56659de Removed -x and -y options
The -x and -y options now stand for --xlabel and --ylabel.

These options should be used to specify the series in the future.
2021-06-17 07:47:14 +09:00
kojix2
858792fa99 Fix a typo 2021-06-14 13:08:45 +09:00
kojix2
e7079c56a2 Update README.md 2021-06-14 13:07:29 +09:00
kojix2
bb8a16a327 Swap the order of count and color in help 2021-06-14 11:37:06 +09:00
kojix2
be0f706231 Update README.md 2021-06-14 11:23:52 +09:00
kojix2
e5c87fbe6f Add recommended tools to README.md 2021-06-11 10:48:33 +09:00
10 changed files with 112 additions and 107 deletions

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@@ -13,6 +13,5 @@ jobs:
- uses: ruby/setup-ruby@v1 - uses: ruby/setup-ruby@v1
with: with:
ruby-version: ${{ matrix.ruby }} ruby-version: ${{ matrix.ruby }}
- run: gem install bundler bundler-cache: true
- run: bundle install
- run: bundle exec rake test - run: bundle exec rake test

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@@ -4,3 +4,9 @@ source 'https://rubygems.org'
# Specify your gem's dependencies in youplot.gemspec # Specify your gem's dependencies in youplot.gemspec
gemspec gemspec
group :test do
gem 'rake'
gem 'simplecov'
gem 'test-unit'
end

143
README.md
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@@ -1,18 +1,15 @@
<div align="center"> <div align="center">
<img src="logo.svg" width="66%" height="66%" /> <img src="logo.svg">
<hr> <hr>
<img alt="Build Status" src="https://github.com/red-data-tools/YouPlot/workflows/test/badge.svg">
<a href="https://rubygems.org/gems/youplot/"><img alt="Gem Version" src="https://badge.fury.io/rb/youplot.svg"></a>
<a href="https://zenodo.org/badge/latestdoi/283230219"><img alt="DOI" src="https://zenodo.org/badge/283230219.svg"></a>
<a href="https://rubydoc.info/gems/youplot/"><img alt="Docs Stable" src="https://img.shields.io/badge/docs-stable-blue.svg"></a>
<a href="LICENSE.txt"><img alt="The MIT License" src="https://img.shields.io/badge/license-MIT-blue.svg"></a>
![Build Status](https://github.com/red-data-tools/YouPlot/workflows/test/badge.svg) YouPlot is a command line tool that draws plots on the terminal.
[![Gem Version](https://badge.fury.io/rb/youplot.svg)](https://badge.fury.io/rb/youplot)
[![Docs Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://rubydoc.info/gems/youplot)
[![The MIT License](https://img.shields.io/badge/license-MIT-blue.svg)](LICENSE.txt)
[![DOI](https://zenodo.org/badge/283230219.svg)](https://zenodo.org/badge/latestdoi/283230219)
YouPlot is a command line tool that draws plots in a terminal.
:bar_chart: Powered by [UnicodePlot](https://github.com/red-data-tools/unicode_plot.rb) :bar_chart: Powered by [UnicodePlot](https://github.com/red-data-tools/unicode_plot.rb)
</div> </div>
## Installation ## Installation
@@ -23,8 +20,9 @@ gem install youplot
## Quick Start ## Quick Start
* `cat data.tsv | uplot <command> [options]` or <img alt="barplot" src="https://user-images.githubusercontent.com/5798442/101999903-d36a2d00-3d24-11eb-9361-b89116f44122.png" width=160> <img alt="histogram" src="https://user-images.githubusercontent.com/5798442/101999820-21cafc00-3d24-11eb-86db-e410d19b07df.png" width=160> <img alt="scatter" src="https://user-images.githubusercontent.com/5798442/101999827-27284680-3d24-11eb-9903-551857eaa69c.png" width=160> <img alt="density" src="https://user-images.githubusercontent.com/5798442/101999828-2abbcd80-3d24-11eb-902c-2f44266fa6ae.png" width=160> <img alt="boxplot" src="https://user-images.githubusercontent.com/5798442/101999830-2e4f5480-3d24-11eb-8891-728c18bf5b35.png" width=160>
* `uplot <command> [options] <data.tsv>`
`uplot <command> [options] <data.tsv>`
### barplot ### barplot
@@ -36,7 +34,7 @@ curl -sL https://git.io/ISLANDScsv \
``` ```
<p align="center"> <p align="center">
<img alt="barplot" src="https://user-images.githubusercontent.com/5798442/101999903-d36a2d00-3d24-11eb-9361-b89116f44122.png"> <img alt="barplot" src="https://user-images.githubusercontent.com/5798442/101999903-d36a2d00-3d24-11eb-9361-b89116f44122.png">
</p> </p>
### histogram ### histogram
@@ -103,10 +101,6 @@ curl -sL https://git.io/IRIStsv \
### count ### count
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.
* https://www.gencodegenes.org/human/
```sh ```sh
cat gencode.v35.annotation.gff3 \ cat gencode.v35.annotation.gff3 \
| grep -v '#' | grep 'gene' | cut -f1 \ | grep -v '#' | grep 'gene' | cut -f1 \
@@ -117,23 +111,21 @@ cat gencode.v35.annotation.gff3 \
<img alt="count" src="https://user-images.githubusercontent.com/5798442/101999832-30b1ae80-3d24-11eb-96fe-e5000bed1f5c.png"> <img alt="count" src="https://user-images.githubusercontent.com/5798442/101999832-30b1ae80-3d24-11eb-96fe-e5000bed1f5c.png">
</p> </p>
In this example, YouPlot counts the number of chromosomes where genes are located.
* [GENCODE - Human Release](https://www.gencodegenes.org/human/)
Note: `count` is not very fast because it runs in a Ruby script. Note: `count` is not very fast because it runs in a Ruby script.
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. 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.
```sh ```sh
cat gencode.v35.annotation.gff3 | grep -v '#' | grep 'gene' | cut -f1 \ cat gencode.v35.annotation.gff3 | grep -v '#' | grep 'gene' | cut -f1 \
| sort | uniq -c | sort -nrk2 | awk '{print $2,$1}' \ | sort | uniq -c | sort -nrk1 \
| uplot bar -d ' ' -t "The number of human gene annotations per chromosome" -c blue | uplot bar --fmt yx -d ' ' -t "The number of human gene annotations per chromosome" -c blue
``` ```
## 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.
@@ -143,18 +135,7 @@ YouPlot is a command line tool for this purpose. With YouPlot, you can continue
| `uplot <command> [options] data.tsv ...` | Take input from files | | `uplot <command> [options] data.tsv ...` | Take input from files |
| `pipeline1 \| uplot <command> -O \| pipeline2` | Outputs data from stdin to stdout | | `pipeline1 \| uplot <command> -O \| pipeline2` | Outputs data from stdin to stdout |
### Where to output the plot? ### Subcommands
By default, the plot is output to *standard error output*.
The output file or stream for the plot can be specified with the `-o` option.
### Where to output the input data?
By default, the input data is not shown anywhere.
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.
### What types of plots are available?
The following sub-commands are available. The following sub-commands are available.
@@ -167,66 +148,75 @@ 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 | `.
### What if the header line is included? ### Output the input data
If your input data contains a header line, you need to specify the `-H` option. * `-O`
* 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.
### How to specify the delimiter? ### Header
Use the `-d` option. To specify a blank space, you can use `uplot bar -d ' ' data.txt`. * `-H`
You do not need to use `-d` option for tab-delimited text since the default value is tab. * If input data contains a header line, you need to specify the `-H` option.
### Is there a way to specify a column as the x-axis or y-axis? ### Delimiter
Not yet. * `-d`
YouPlot treats the first column as the X axis and the second column as the Y axis. * You do not need to use `-d` option for tab-delimited text since the default value is tab.
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. * To specify a blank space, you can use `uplot bar -d ' ' data.txt`.
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. ### Real-time data
See `youplot <command> --help` for more details.
* Use `awk '{print $2, $1}'` to swap lines. * `-p` `--progress`
* Use `paste` to concatenate series. * Experimental progressive mode is currently under development.
* `ruby -e 'loop{puts rand(100)}' | uplot line --progress`
### How to plot real-time data? ### Show detailed options for subcommands
Experimental progressive mode is currently under development. * `--help`
* The `--help` option will show more detailed options for each subcommand.
* `uplot hist --help`
```sh ### Set columns as x-axis or y-axis
ruby -e 'loop{puts rand(100)}' | uplot line --progress
```
### How to view detailed command line options? * 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.
* 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.
Use `--help` to print command-specific options. * `--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 might be used to specify columns in the future.
`uplot hist --help` * Use `awk '{print $2, $1}'` to swap columns. Use `paste` to concatenate series.
``` ### Categorical data
Usage: uplot histogram [options] <in.tsv>
Options for histogram: * With GNU datamash, you can manage to handle categorized data.
--symbol VAL character to be used to plot the bars * `cat test/fixtures/iris.csv | sed '/^$/d' | datamash --header-in --output-delimiter=: -t, -g5 collapse 3,4 | cut -f2-3 -d: | sed 's/:/\n/g' | uplot s -d, -T --fmt xyxy`
--closed VAL side of the intervals to be closed [left] * This is not so easy...
-n, --nbins VAL approximate number of bins
Options: ### Time series
...
```
### How to view the list of available colors? * Not yet supported.
```sh ## Tools that are useful to use with YouPlot
uplot colors
``` * [csvtk](https://github.com/shenwei356/csvtk)
* [GNU datamash](https://www.gnu.org/software/datamash/)
* [awk](https://www.gnu.org/software/gawk/)
* [xsv](https://github.com/BurntSushi/xsv)
## Contributing ## Contributing
@@ -248,6 +238,7 @@ 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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@@ -6,6 +6,12 @@ require_relative 'youplot/parameters'
require_relative 'youplot/command' require_relative 'youplot/command'
module YouPlot module YouPlot
# @run_as_executable = true / false
# YouPlot behaves slightly differently when run as a command line tool
# and when run as a script (e.g. for testing). In the event of an error,
# when run as a command line tool, YouPlot will display a short error message
# and exit abnormally. When run as a script, it will just raise an error.
@run_as_executable = false
class << self class << self
attr_accessor :run_as_executable attr_accessor :run_as_executable
@@ -13,5 +19,4 @@ module YouPlot
@run_as_executable @run_as_executable
end end
end end
@run_as_executable = false
end end

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@@ -6,6 +6,27 @@
require_relative 'processing' require_relative 'processing'
require 'unicode_plot' require 'unicode_plot'
# If the line color is specified as a number, the program will display an error
# message to the user and exit. Remove this patch when UnicodePlot is improved.
module UnicodePlot
class << self
alias lineplot_original lineplot
def lineplot(*args, **kw)
if kw[:color].is_a? Numeric
warn <<~EOS
YouPlot: Line colors cannot be specified by numerical values.
For more information, please see the following issue.
https://github.com/red-data-tools/unicode_plot.rb/issues/34
EOS
YouPlot.run_as_executable ? exit(1) : raise(Error)
end
lineplot_original(*args, **kw)
end
end
end
module YouPlot module YouPlot
# plotting functions. # plotting functions.
module Backends module Backends
@@ -106,11 +127,10 @@ module YouPlot
def plot_xyxy(data, method1, params) def plot_xyxy(data, method1, params)
headers = data.headers headers = data.headers
series = data.series series2 = data.series
.map { |s| s.map(&:to_f) }
.each_slice(2).to_a
method2 = get_method2(method1) method2 = get_method2(method1)
series.map! { |s| s.map(&:to_f) }
series2 = series.each_slice(2).to_a
series = nil
params.name ||= headers[0] if headers params.name ||= headers[0] if headers
params.xlim ||= series2.map(&:first).flatten.minmax # why need? params.xlim ||= series2.map(&:first).flatten.minmax # why need?
params.ylim ||= series2.map(&:last).flatten.minmax # why need? params.ylim ||= series2.map(&:last).flatten.minmax # why need?
@@ -182,7 +202,7 @@ module YouPlot
series = data.series series = data.series
if series.size == 1 if series.size == 1
warn <<~EOS warn <<~EOS
youplot: There is only one series of input data. Please check the delimiter. YouPlot: There is only one series of input data. Please check the delimiter.
Headers: \e[35m#{data.headers.inspect}\e[0m Headers: \e[35m#{data.headers.inspect}\e[0m
The first item is: \e[35m\"#{series[0][0]}\"\e[0m The first item is: \e[35m\"#{series[0][0]}\"\e[0m

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@@ -169,7 +169,7 @@ module YouPlot
def output_data(input) def output_data(input)
# Pass the input to subsequent pipelines # Pass the input to subsequent pipelines
case options[:pass] case options[:pass]
when IO when IO, StringIO
options[:pass].print(input) options[:pass].print(input)
else else
if options[:pass] if options[:pass]

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@@ -58,10 +58,10 @@ module YouPlot
parser.on('-t', '--title STR', String, 'print string on the top of plot') do |v| parser.on('-t', '--title STR', String, 'print string on the top of plot') do |v|
params.title = v params.title = v
end end
parser.on('-x', '--xlabel STR', String, 'print string on the bottom of the plot') do |v| parser.on('--xlabel STR', String, 'print string on the bottom of the plot') do |v|
params.xlabel = v params.xlabel = v
end end
parser.on('-y', '--ylabel STR', String, 'print string on the far left of the plot') do |v| parser.on('--ylabel STR', String, 'print string on the far left of the plot') do |v|
params.ylabel = v params.ylabel = v
end end
parser.on('-w', '--width INT', Numeric, 'number of characters per row') do |v| parser.on('-w', '--width INT', Numeric, 'number of characters per row') do |v|
@@ -95,7 +95,7 @@ module YouPlot
parser.on('-M', '--monochrome', TrueClass, 'no colouring even if writing to a tty') do |_v| parser.on('-M', '--monochrome', TrueClass, 'no colouring even if writing to a tty') do |_v|
UnicodePlot::IOContext.define_method(:color?) { false } # FIXME UnicodePlot::IOContext.define_method(:color?) { false } # FIXME
end end
parser.on('--encoding STR', String, 'Specify the input encoding') do |v| parser.on('--encoding STR', String, 'specify the input encoding') do |v|
options[:encoding] = v options[:encoding] = v
end end
# Optparse adds the help option, but it doesn't show up in usage. # Optparse adds the help option, but it doesn't show up in usage.
@@ -130,10 +130,9 @@ module YouPlot
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
colors color show the list of available colors
count c draw a baplot based on the number of count c draw a baplot based on the number of
occurrences (slow) occurrences (slow)
colors color show the list of available colors
General options: General options:
--help print command specific help menu --help print command specific help menu

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@@ -1,5 +1,5 @@
# frozen_string_literal: true # frozen_string_literal: true
module YouPlot module YouPlot
VERSION = '0.4.2' VERSION = '0.4.3'
end end

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@@ -155,21 +155,11 @@ class YouPlotSimpleTest < Test::Unit::TestCase
assert_equal fixture('simple-lineplot-xlabel.txt'), @stderr_file.read assert_equal fixture('simple-lineplot-xlabel.txt'), @stderr_file.read
end end
test :line_x do
YouPlot::Command.new(['line', '-x', 'X-LABEL']).run
assert_equal fixture('simple-lineplot-xlabel.txt'), @stderr_file.read
end
test :line_ylabel do test :line_ylabel do
YouPlot::Command.new(['line', '--ylabel', 'Y-LABEL']).run YouPlot::Command.new(['line', '--ylabel', 'Y-LABEL']).run
assert_equal fixture('simple-lineplot-ylabel.txt'), @stderr_file.read assert_equal fixture('simple-lineplot-ylabel.txt'), @stderr_file.read
end end
test :line_y do
YouPlot::Command.new(['line', '-y', 'Y-LABEL']).run
assert_equal fixture('simple-lineplot-ylabel.txt'), @stderr_file.read
end
test :line_width do test :line_width do
YouPlot::Command.new(['line', '--width', '17']).run YouPlot::Command.new(['line', '--width', '17']).run
assert_equal fixture('simple-lineplot-width-17.txt'), @stderr_file.read assert_equal fixture('simple-lineplot-width-17.txt'), @stderr_file.read

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@@ -19,10 +19,5 @@ Gem::Specification.new do |spec|
spec.executables = %w[uplot youplot] spec.executables = %w[uplot youplot]
spec.require_paths = ['lib'] spec.require_paths = ['lib']
spec.add_runtime_dependency 'unicode_plot' spec.add_dependency 'unicode_plot', '>= 0.0.5'
spec.add_development_dependency 'bundler'
spec.add_development_dependency 'rake'
spec.add_development_dependency 'rubocop'
spec.add_development_dependency 'simplecov'
spec.add_development_dependency 'test-unit'
end end