diff --git a/README.md b/README.md index 9841b5f..2afb335 100644 --- a/README.md +++ b/README.md @@ -107,19 +107,36 @@ cat gencode.v35.annotation.gff3 | grep -v '#' | grep 'gene' | cut -f1 \ ## Usage +### Why YouPlot? + +Wouldn't it be a bit of 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 same as `youplot`. You can use either. +`uplot` is the shortened form of `youplot`. You can use either. | | | |-----------------------------------|------------------------------------------------| | Reads data from standard input | `cat data.tsv \| uplot [options]` | -| Reads data from a file | `uplot [options] data.tsv` | +| Reads data from files | `uplot [options] data.tsv ...` | | Outputs data from stdin to stdout | `pipeline1 \| uplot -O \| pipeline2` | -### plot commands +### Where to output the plot? -| command | short | | +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 output 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 + +| command | short | how it works | |-----------|-------|----------------------------------------| | barplot | bar | draw a horizontal barplot | | histogram | hist | draw a horizontal histogram | @@ -129,8 +146,13 @@ cat gencode.v35.annotation.gff3 | grep -v '#' | grep 'gene' | cut -f1 \ | density | d | draw a density plot | | boxplot | box | draw a horizontal boxplot | +See Quick Start for `count`. -### help +| command | short | how it works | +|-----------|-------|----------------------------------------------------------| +| count | c | draw a baplot based on the number of occurrences (slow) | + +### How to view detailed command line options Use `--help` to print command-specific options. @@ -148,27 +170,12 @@ Options: ... ``` -### colors +### How to view the list of available colors? ```sh uplot colors ``` -## Why YouPlot? - -Wouldn't it be a bit of 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. - -## Development - -```sh -git clone https://github.com/your_name/GR.rb # Clone the Git repo -cd GR.rb -bundle install # Install the gem dependencies -bundle exec rake test # Run the test -bundle exec rake install # Installation from source code -``` - ## Contributing * [Report bugs](https://github.com/kojix2/youplot/issues) @@ -176,6 +183,17 @@ bundle exec rake install # Installation from source code * Write, clarify, or fix documentation * Suggest or add new features + +### Development + +```sh +git clone https://github.com/your_name/GR.rb # Clone the Git repo +cd GR.rb +bundle install # Install the gem dependencies +bundle exec rake test # Run the test +bundle exec rake install # Installation from source code +``` + ## License [MIT License](https://opensource.org/licenses/MIT).