### Install pyGenomeTracks from Source

Source: https://github.com/deeptools/pygenometracks/blob/master/docs/content/installation.rst

Manually clone or download the source code and install it using the setup script.

```bash
$ git clone https://github.com/deeptools/pyGenomeTracks.git
```

```bash
$ wget https://github.com/deeptools/pyGenomeTracks/archive/3.1.tar.gz
$ tar -xzvf
```

```bash
$ python setup.py install --prefix /User/Tools/pyGenomeTracks3.1
```

--------------------------------

### Install pyGenomeTracks via Galaxy API

Source: https://github.com/deeptools/pygenometracks/blob/master/docs/content/installation.rst

Automate the installation of the tool into a local Galaxy instance using the provided installation script.

```bash
$ python ./scripts/api/install_tool_shed_repositories.py \
		--api YOUR_API_KEY -l http://localhost/ \
		--url http://toolshed.g2.bx.psu.edu/ \
		-o iuc -r <revision> --name pygenometracks \
		--tool-deps --repository-deps --panel-section-name plots
```

--------------------------------

### Install pyGenomeTracks via Pip

Source: https://github.com/deeptools/pygenometracks/blob/master/docs/content/installation.rst

Install the package using pip, optionally specifying a custom installation prefix.

```bash
$ pip install pyGenomeTracks
```

```bash
$ pip install --install-option="--prefix=/MyPath/Tools/pyGenomeTracks" git+https://github.com/deeptools/pyGenomeTracks.git
```

--------------------------------

### Install pyGenomeTracks via Mamba

Source: https://github.com/deeptools/pygenometracks/blob/master/docs/content/installation.rst

Use mamba for faster dependency resolution when creating the environment and installing the package.

```bash
$ conda create -n pygenometracks -c bioconda -c conda-forge mamba python=3.9
$ conda activate pygenometracks
$ mamba install -c conda-forge -c bioconda pygenometracks
```

```bash
$ conda create -n pygenometracks -c bioconda -c conda-forge mamba python=3.7
$ conda activate pygenometracks
$ mamba install -c conda-forge -c bioconda pygenometracks=3.5
```

--------------------------------

### Install pyGenomeTracks via Conda

Source: https://github.com/deeptools/pygenometracks/blob/master/docs/content/installation.rst

Use conda to create a dedicated environment and install the package from bioconda and conda-forge channels.

```bash
$ conda create -n pygenometracks -c bioconda -c conda-forge pygenometracks
```

```bash
$ conda create -n pygenometracks -c bioconda -c conda-forge pygenometracks=3.5 python=3.7
```

--------------------------------

### Visualizing Epilogos

Source: https://github.com/deeptools/pygenometracks/blob/master/docs/content/examples.rst

Visualize epigenetic states using epilogos, requiring a qcat file.

```INI
epilogos_track.ini
```

```bash
$ pyGenomeTracks  --tracks epilogos_track.ini --region X:3100000-3150000 -o epilogos_track.png
```

--------------------------------

### Run pyGenomeTracks with custom configuration

Source: https://github.com/deeptools/pygenometracks/blob/master/docs/content/adding-new-tracks.rst

Execute the pyGenomeTracks command using a custom configuration file and specified genomic region.

```bash
$ pyGenomeTracks  --tracks new_track.ini --region X:3000000-3200000 -o new_track.png
```

```bash
$ pyGenomeTracks  --tracks bedgraph_matrix.ini --region X:2000000-3500000 -o bedgraph_matrix.png
```

--------------------------------

### Basic Bedgraph Plotting

Source: https://github.com/deeptools/pygenometracks/blob/master/docs/content/examples.rst

Execute a basic plot using a bedgraph configuration file.

```bash
$ pyGenomeTracks --tracks bedgraph_useMid.ini --BED regions_imbricated_chr2.bed --trackLabelFraction 0.2 --width 38 --dpi 130  -o master_bedgraph_useMid.png
```

--------------------------------

### Comprehensive Track Overlay

Source: https://github.com/deeptools/pygenometracks/blob/master/docs/content/examples.rst

Combine multiple tracks using overlay parameters in the configuration.

```INI
browser_tracks.ini
```

```bash
$ pyGenomeTracks  --tracks browser_tracks.ini --region X:3000000-3500000 --trackLabelFraction 0.2 --width 38 --dpi 130  -o master_plot.png
```

--------------------------------

### Epilogos Track Configuration Parameters

Source: https://github.com/deeptools/pygenometracks/blob/master/docs/content/tracks/auto/epilogos_options_text.txt

Standard configuration settings for an Epilogos track definition.

```ini
title =
height = 2
# orientation = inverted
#overlay_previous = yes
categories_file = <path to json categories file>
file_type = epilogos
```

--------------------------------

### Bigwig Track Visualization

Source: https://github.com/deeptools/pygenometracks/blob/master/docs/content/examples.rst

Plot bigwig data tracks with specific configuration settings.

```INI
bigwig.ini
```

```bash
$ pyGenomeTracks  --tracks bigwig.ini --region X:2700000-3100000 --trackLabelFraction 0.2 --dpi 130 -o master_bigwig.png
```

--------------------------------

### Customizing Epilogos Colors

Source: https://github.com/deeptools/pygenometracks/blob/master/docs/content/examples.rst

Define custom colors for epilogos using a JSON configuration file.

```JSON
epilog_cats.json
```

```INI
epilogos_track2.ini
```

```bash
$ pyGenomeTracks  --tracks epilogos_track2.ini --region X:3100000-3150000 -o epilogos_track2.png
```

--------------------------------

### Generate Hi-C overlay plot

Source: https://github.com/deeptools/pygenometracks/blob/master/docs/content/examples.rst

Command to generate a plot with overlay tracks using a specified configuration file.

```bash
$ pyGenomeTracks  --tracks browser_tracks_hic.ini --region X:2500000-3500000 --trackLabelFraction 0.23 --width 38 --dpi 130 -o master_plot_hic.png
```

--------------------------------

### Plotting Peaks with MACS2 Format

Source: https://github.com/deeptools/pygenometracks/blob/master/docs/content/examples.rst

Visualize peaks using the narrowPeak format defined in an INI configuration.

```INI
narrow_peak2.ini
```

```bash
$ pyGenomeTracks --tracks narrow_peak2.ini --region X:2760000-2802000 --trackLabelFraction 0.2 --dpi 130 -o master_narrowPeak2.png
```

--------------------------------

### Hi-C Data Plotting

Source: https://github.com/deeptools/pygenometracks/blob/master/docs/content/examples.rst

Visualize Hi-C data overlaid with TADs and bigwig tracks.

```INI
hic_track.ini
```

```bash
$ pyGenomeTracks --tracks hic_track.ini -o hic_track.png --region chrX:2500000-3500000
```

--------------------------------

### Generate log1p transformation plot

Source: https://github.com/deeptools/pygenometracks/blob/master/docs/content/examples.rst

Command to generate a plot with log1p transformation applied to the data.

```bash
$ pyGenomeTracks --tracks log1p.ini --region X:2700000-3100000 --trackLabelFraction 0.2 --dpi 130 -o master_log1p.png
```

--------------------------------

### Hi-C Rasterization and Height Control

Source: https://github.com/deeptools/pygenometracks/blob/master/docs/content/examples.rst

Control heatmap rasterization and track height for Hi-C plots.

```INI
browser_tracks_hic_rasterize_height.ini
```

```bash
$ pyGenomeTracks --tracks browser_tracks_hic_rasterize_height.ini --region X:2500000-2600000 --trackLabelFraction 0.23 --width 38 --dpi 10 -o master_plot_hic_rasterize_height.pdf
```

--------------------------------

### Epilogos Categories JSON Structure

Source: https://github.com/deeptools/pygenometracks/blob/master/docs/content/tracks/auto/epilogos_options_text.txt

The expected JSON format for mapping category IDs to labels and colors.

```json
{
"categories":{
          "1":["Active TSS","#ff0000"],
          "2":["Flanking Active TSS","#ff4500"],
          "3":["Transcr at gene 5" and 3"","#32cd32"],
          "4":["Strong transcription","#008000"],
          "5":["Weak transcription","#006400"]
	}
}
```

--------------------------------

### Generate operation plot

Source: https://github.com/deeptools/pygenometracks/blob/master/docs/content/examples.rst

Command to generate a plot performing operations between files defined in the configuration.

```bash
$ pyGenomeTracks --tracks operation.ini --region X:2700000-3100000 --trackLabelFraction 0.2 --dpi 130 -o master_operation.png
```

--------------------------------

### Plotting with Horizontal Lines

Source: https://github.com/deeptools/pygenometracks/blob/master/docs/content/examples.rst

Add horizontal lines to a genomic track plot.

```INI
hlines.ini
```

```bash
$ pyGenomeTracks --tracks hlines.ini --region X:2700000-3100000 --trackLabelFraction 0.2 --dpi 130 -o master_hlines.png
```

--------------------------------

### Generate log transformation plot

Source: https://github.com/deeptools/pygenometracks/blob/master/docs/content/examples.rst

Command to generate a plot with log transformation applied, noting that y-axis labels are omitted.

```bash
$ pyGenomeTracks --tracks log.ini  --region chr2:73,800,000-75,744,000 --trackLabelFraction 0.2 --width 38 --dpi 130  -o master_log.png
```

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