gtracks 1.12.6
Plot genome track data
Requires Python: >=3.7

# gtracks

Plot genome track data from bigWig and bedGraph files. Powered by [pyGenomeTracks](https://github.com/deeptools/pyGenomeTracks).

## Installation

```sh
pip install gtracks
```
or
```sh
pip install --user gtracks
```

### In conda

```sh
conda create -n gtracks -c conda-forge -c bioconda deeptools seaborn pybedtools gff2bed
conda activate gtracks
mamba install -c conda-forge -c bioconda pygenometracks
pip install gtracks
```

## Examples

An example bigwig file with ATAC-seq data from the insulin region is included.
You can generate a test plot like this:
```sh
gtracks INS-IGF2 test.png
```
![test plot](https://gitlab.com/salk-tm/gtracks/-/raw/master/test.png)

You can plot your own tracks over other genomic regions by providing more
positional arguments: a region or gene name and paths to one or more bigWig
files. The file type of the plot will be determined by the
output file extension.
```sh
gtracks chr11:2150341-2182439 track1.bw track2.bw output.pdf
gtracks INS track1.bw track2.bw output.svg
```

### Modifying the gene annotations track

GRCh37/hg19 gene annotations are used by default, but you can plot GRCh38/hg38
genes by adding `--genes GRCh38` or `--genes hg38`. You can use your own gene
annotations file (BED or BED12 format) by providing
`--genes <path/to/genes.bed.gz>`.

You may want to add more rows to the genes track. You can do this using
the `--genes-height` and `--gene-rows` options.

```sh
gtracks INS test-genes.png --genes-height 6 --gene-rows 6
```
![test plot with more gene rows](https://gitlab.com/salk-tm/gtracks/-/raw/master/test-genes.png)

### Coordinate parsing

By default, `gtracks` parses input coordinates according to the following regular expression:

```([Cc]hr)?[0-9XYZWM]+:[0-9]+-[0-9]+$```

Inputs not matching this expression are interpreted as gene names. This can cause errors
if e.g. your contig names do not match the format. To change how coordinates are parsed,
you can supply an alternative regular expression using the `--coord-regex` option. For example, the following expression
allows arbitrary contig names:

```--coord-regex '[\s\S]+:[0-9]+-[0-9]+$'```

### Changing the color palette

You can change the color palette for bigWig tracks using the `--color-palette` option.
```sh
gtracks INS track1.bw track2.bw track3.bw output.pdf --color-palette "#color1" "#color2" "#color3"
```

### Setting y-axis height

By default, tracks have different y-axis heights depending on signal height.
You can set a uniform y-axis height for all tracks using the `--max` option.

```sh
gtracks INS track1.bw track2.bw track3.bw output.pdf --max 400
```

For more command-line options, see the usage page below.

### Example with non-human data and BED track

This example command uses data from _S. polyrhiza_ and includes a BED track.

```sh
gtracks --genes Sp9512 7:6975000-6989000 sp9512_frond_example.bw sp9512_turion_example.bw sp9512_frond_turion_dmr.bed test-non-human.png
```

![test plot non human](https://gitlab.com/salk-tm/gtracks/-/raw/master/test-non-human.png)

## Environment variables

If you want to use your own bigWig files but don't want to write out their
paths every time you run `gtracks`, you can set your own default tracks using
the environment variable `GTRACKS_TRACKS`.
```sh
export GTRACKS_TRACKS=track1.bw,track2.bw,track3.bw
gtracks output.pdf
```

You can also change the default gene annotations file and color palette using
environment variables `GTRACKS_GENES_PATH` and `GTRACKS_COLOR_PALETTE`.
```sh
export GTRACKS_GENES_PATH=path/to/genes.bed.gz
export GTRACKS_COLOR_PALETTE="#color1,#color2,#color3"
gtracks output.pdf
```

Should your genomic coordinates take a different form from the included default
regex, you may set a different default regex using `GTRACKS_COORD_REGEX`:
```sh
export GTRACKS_COORD_REGEX='[\s\S]+:[0-9]+-[0-9]+$'
```

## Usage

```
usage: gtracks [-h] [--genes <{path/to/genes.bed.gz,GRCh37,GRCh38,hg19,hg38,Sp9512}>]
               [--color-palette <#color> [<#color> ...]] [--max <float>] [--tmp-dir <temp/file/dir>] [--width <int>]
               [--genes-height <int>] [--gene-rows <int>] [--x-axis {top,bottom,none}]
               [--vlines-bed <path/to/vlines.bed>] [--bed-labels]
               <{chr:start-end,GENE}> [<track.{bw,bed}> [<track.{bw,bed}> ...]] <path/to/output.{pdf,png,svg}>

Plot bigWig, bedGraph, and BED signal tracks with gene annotations in a genomic region

positional arguments:
  <{chr:start-end,GENE}>
                        coordinates or gene name to plot
  <track.{bw,bdg,bed}>      bigWig, bedGraph, or bed files containing tracks
  <path/to/output.{pdf,png,svg}>
                        path to output file

optional arguments:
  -h, --help            show this help message and exit
  --genes <{path/to/genes.bed.gz,GRCh37,GRCh38,hg19,hg38,Sp9512}>
                        compressed 6-column BED file or 12-column BED12 file containing gene annotations. Alternatively,
                        providing a genome identifier will use one of the included gene tracks. (default: GRCh37)
  --flank <int>         add flanks to the plotting region
  --color-palette <#color> [<#color> ...]
                        color pallete for tracks
  --max <float>         max value of y-axis
  --tmp-dir <temp/file/dir>
                        directory for temporary files
  --width <int>         width of plot in cm (default: 40)
  --genes-height <int>  height of genes track (default: 2)
  --gene-rows <int>     number of gene rows (default: 1)
  --x-axis {top,bottom,none}
                        where to draw the x-axis (default: top)
  --vlines-bed <path/to/vlines.bed>
                        BED file defining vertical lines
  --bed-labels          include labels on BED tracks
  --coord-regex <regex>
                        regular expression indicating the format for coordinates (default: ([Cc]hr)?[0-9XY]+:[0-9]+-[0-9]+$)
```