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@ -9,7 +9,7 @@
[![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.
YouPlot is a command line tool that draws plots in the terminal.
:bar_chart: Powered by [UnicodePlot](https://github.com/red-data-tools/unicode_plot.rb)
@ -23,8 +23,7 @@ gem install youplot
## Quick Start
* `cat data.tsv | uplot <command> [options]` or
* `uplot <command> [options] <data.tsv>`
`uplot <command> [options] <data.tsv>`
### barplot
@ -103,10 +102,6 @@ curl -sL https://git.io/IRIStsv \
### 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
cat gencode.v35.annotation.gff3 \
| grep -v '#' | grep 'gene' | cut -f1 \
@ -117,13 +112,16 @@ cat gencode.v35.annotation.gff3 \
<img alt="count" src="https://user-images.githubusercontent.com/5798442/101999832-30b1ae80-3d24-11eb-96fe-e5000bed1f5c.png">
</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.
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
cat gencode.v35.annotation.gff3 | grep -v '#' | grep 'gene' | cut -f1 \
| sort | uniq -c | sort -nrk2 | awk '{print $2,$1}' \
| uplot bar -d ' ' -t "The number of human gene annotations per chromosome" -c blue
| sort | uniq -c | sort -nrk1 \
| uplot bar --fmt yx -d ' ' -t "The number of human gene annotations per chromosome" -c blue
```
## Usage
@ -143,18 +141,7 @@ YouPlot is a command line tool for this purpose. With YouPlot, you can continue
| `uplot <command> [options] data.tsv ...` | Take input from files |
| `pipeline1 \| uplot <command> -O \| pipeline2` | Outputs data from stdin to stdout |
### Where to output the plot?
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?
### Subcommands
The following sub-commands are available.
@ -174,6 +161,17 @@ See Quick Start for `count`.
|-----------|-------|----------------------------------------------------------|
| count | c | draw a barplot based on the number of occurrences (slow) |
### Where to output the plot?
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 if the header line is included?
If your input data contains a header line, you need to specify the `-H` option.