pyGenomeTracks

https://pygenometracks.readthedocs.io/en/latest/
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pyGenomeTracks is a standalone program and library to plot highly customizable genome browser tracks...
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### Install pygenometracks from Source

Source: https://pygenometracks.readthedocs.io/en/latest/content/installation

Installs pyGenomeTracks from its source code. This involves cloning the repository, downloading a specific release, and then installing using `setup.py`. It allows specifying an installation prefix.

```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://pygenometracks.readthedocs.io/en/latest/content/installation

Installs pyGenomeTracks into a Galaxy server using the Galaxy API. This method requires an API key and specifies repository details, including dependencies and panel section.

```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

```

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

### Run PyGenomeTracks with Transparency Overlay Example

Source: https://pygenometracks.readthedocs.io/en/latest/content/examples

This command executes PyGenomeTracks using a configuration file demonstrating complex overlays with transparency for bigwig tracks.

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

```

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

### Run PyGenomeTracks Demo Example 1

Source: https://pygenometracks.readthedocs.io/en/latest/content/examples

This command runs PyGenomeTracks with the 'demo.ini' configuration file to visualize a relatively large genomic region.

```bash
$ pyGenomeTracks --tracks demo.ini --region chrX:3000000-3500000 -o demo.png

```

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

### Run PyGenomeTracks Demo Example 2

Source: https://pygenometracks.readthedocs.io/en/latest/content/examples

This command executes PyGenomeTracks with the 'demo2.ini' configuration file, which includes vertical lines and highlights for a smaller genomic region.

```bash
$ pyGenomeTracks --tracks demo2.ini --region chrX:3320000-3370000 -o demo2.png

```

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

### Install pygenometracks with Pip

Source: https://pygenometracks.readthedocs.io/en/latest/content/installation

Installs pyGenomeTracks using pip. This method automatically installs Python requirements but requires manual installation of BEDTools. It also shows how to specify an installation prefix.

```bash
$ pip install pyGenomeTracks

```

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

```

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

### PyGenomeTracks: Configuration for BED tracks with arrowhead options

Source: https://pygenometracks.readthedocs.io/en/latest/content/examples

This configuration demonstrates how to display BED files with options for arrowhead placement. It shows examples with default arrowhead behavior and when the arrowhead is included inside the interval using 'arrowhead_included = true'.

```ini
[x-axis]
where = top
title = where =top

[spacer]
height = 0.05

[genes 2]
file = dm3_genes.bed.gz
height = 3
title = genes (bed12) style = UCSC; fontsize = 10
style = UCSC
fontsize = 10

[genes 2bis]
file = dm3_genes.bed.gz
height = 3
title = genes (bed12) style = UCSC; arrow_interval=10; fontsize = 10
style = UCSC
arrow_interval = 10
fontsize = 10

[spacer]
height = 1

[test bed6]
file = dm3_genes.bed6.gz
height = 3
title = bed6 border_color = black; fontsize=8; color=red
fontsize = 8
file_type = bed
color = red
border_color = black

[spacer]
height = 1

[test bed6 arrowhead_included]
file = dm3_genes.bed6.gz
height = 3
title = bed6 border_color = black; fontsize=8; color=red; arrowhead_included = true
fontsize = 8
file_type = bed
color = red
border_color = black
arrowhead_included = true

[spacer]
height = 1

[test bed4]
file = dm3_genes.bed4.gz
height = 3
title = bed4 fontsize = 10; line_width = 1.5
fontsize = 10
file_type = bed
line_width = 1.5

[spacer]
height = 1

[test bed]
file = dm3_subset_BDGP5.78_asbed_sorted.bed.gz
height = 8
title = gtf from ensembl in bed12
fontsize = 12
file_type = bed

[spacer]
height = 1

[test bed]
file = dm3_subset_BDGP5.78_asbed_sorted.bed.gz
height = 8
title = gtf from ensembl in bed12; arrowhead_included = true
fontsize = 12
file_type = bed
arrowhead_included = true

[spacer]
height = 1

[x-axis]
fontsize = 30
title = fontsize = 30

[vlines]
type = vlines
file = dm3_genes.bed4.gz
line_style = dotted

[second_vlines]
type = vlines
file = dm3_genes_end.bed
line_width = 1
color = orange
zorder = -100

```

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

### Run pyGenomeTracks for Hi-C Visualization with Overlays

Source: https://pygenometracks.readthedocs.io/en/latest/content/examples

Command-line execution of pyGenomeTracks for visualizing Hi-C data with overlaid tracks. Configures region, label fraction, width, DPI, and output file.

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

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

### Basic BigWig Track Configuration

Source: https://pygenometracks.readthedocs.io/en/latest/content/examples

This configuration defines a single bigwig track with optional height, title, and value range settings. It's a minimal setup for visualizing bigwig data.

```ini
[bigwig file test]
file = bigwig.bw
# height of the track in cm (optional value)
height = 4
title = bigwig
min_value = 0
max_value = 30

```

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

### Run pyGenomeTracks for Hi-C Matrix Visualization

Source: https://pygenometracks.readthedocs.io/en/latest/content/examples

Command-line execution of pyGenomeTracks to generate a Hi-C matrix plot. Requires a configuration file for tracks and specifies the region and output file.

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

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

### Overlaying BigWig Tracks with Transparency

Source: https://pygenometracks.readthedocs.io/en/latest/content/examples

This configuration demonstrates overlaying multiple bigwig tracks with varying transparency (alpha values) and summary methods (max, mean).

```ini
[test bigwig]
file = bigwig2_X_2.5e6_3.5e6.bw
color = blue
height = 7
title = No alpha: (bigwig color=blue 2000 bins) overlaid with (bigwig color = (0.6, 0, 0) max over 300 bins) overlaid with (bigwig mean color = green 200 bins)
number_of_bins = 2000
min_value = 0
max_value = 30

[test bigwig max]
file = bigwig2_X_2.5e6_3.5e6.bw
color = (0.6, 0, 0)
summary_method = max
number_of_bins = 300
overlay_previous = share-y

[test bigwig mean]
file = bigwig2_X_2.5e6_3.5e6.bw
color = green
type = fill
number_of_bins = 200
overlay_previous = share-y

[spacer]

[test bigwig]
file = bigwig2_X_2.5e6_3.5e6.bw
color = blue
height = 7
title = alpha (bigwig color = blue 2000 bins) overlaid with (bigwig color = (0.6, 0, 0) alpha = 0.5 max over 300 bins) overlaid with (bigwig mean color = green alpha = 0.5 200 bins)
number_of_bins = 2000
min_value = 0
max_value = 30

[test bigwig max]
file = bigwig2_X_2.5e6_3.5e6.bw
color = (0.6, 0, 0)
alpha = 0.5
summary_method = max
number_of_bins = 300
overlay_previous = share-y

[test bigwig mean]
file = bigwig2_X_2.5e6_3.5e6.bw
color = green
alpha = 0.5
type = fill
number_of_bins = 200
overlay_previous = share-y

[spacer]

[test bigwig]
file = bigwig2_X_2.5e6_3.5e6.bw
height = 7
title = alpha for lines/points: (bigwig color=(0.6, 0, 0) alpha = 0.5 max) overlaid with (bigwig mean color = green alpha = 0.5 line:2) overlaid with (bigwig min color = blue alpha = 0.5 points:3)
color = (0.6, 0, 0)
alpha = 0.5
summary_method = max
number_of_bins = 300
min_value = 0
max_value = 30

[test bigwig mean]
file = bigwig2_X_2.5e6_3.5e6.bw
color = green
type = line:2
alpha = 0.5
summary_method = mean
number_of_bins = 300
overlay_previous = share-y

[test bigwig min]
file = bigwig2_X_2.5e6_3.5e6.bw
color = blue
summary_method = min
number_of_bins = 1000
type = points:3
alpha = 0.5
overlay_previous = share-y

[x-axis]


```

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

### Run PyGenomeTracks with BigWig and Genes

Source: https://pygenometracks.readthedocs.io/en/latest/content/examples

This command runs PyGenomeTracks with a configuration file that includes both a bigwig track and gene annotations, specifying a region and output file.

```bash
$ pyGenomeTracks --tracks bigwig_with_genes.ini --region X:2,800,000-3,100,000 -o bigwig_with_genes.png

```

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

### Generate Zooms from BED file with pyGenomeTracks

Source: https://pygenometracks.readthedocs.io/en/latest/content/examples

This example demonstrates how to generate genomic visualization zooms using a BED file with pyGenomeTracks. The BED file defines specific regions to be plotted. The command line specifies the track configuration and the BED file containing the regions of interest.

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

```

```bed
track type=bed name=regions_to_plot
chr2	73800000	75744000
chr2	74000000	74800000

```

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

### Configure Hi-C Matrix with Overlaid TADs and Links

Source: https://pygenometracks.readthedocs.io/en/latest/content/examples

INI file configuration for pyGenomeTracks, demonstrating overlaying TADs and links on a Hi-C matrix. Includes settings for track titles, colormaps, transformations, and overlay behavior.

```ini
[hic matrix]
file = Li_et_al_2015.h5
title = depth = 200000; transform = log1p; min_value = 5
depth = 200000
min_value = 5
transform = log1p
file_type = hic_matrix
show_masked_bins = false

[hic matrix]
file = Li_et_al_2015.h5
title = depth = 250000; orientation = inverted; customized colormap; min_value = 5; max_value = 70
min_value = 5
max_value = 70
depth = 250000
colormap = ['white', (1, 0.88, .66), (1, 0.74, 0.25), (1, 0.5, 0), (1, 0.19, 0), (0.74, 0, 0), (0.35, 0, 0)]
file_type = hic_matrix
show_masked_bins = false
orientation = inverted

[spacer]
height = 0.5

[hic matrix]
file = Li_et_al_2015.h5
title = depth = 300000; transform = log1p; colormap Blues (TADs: overlay_previous = share-y; line_width = 1.5)
colormap = Blues
min_value = 10
max_value = 150
depth = 300000
transform = log1p
file_type = hic_matrix

[tads]
file = tad_classification.bed
#title = TADs color = none; border_color = black
file_type = domains
border_color = black
color = none
height = 5
line_width = 1.5
overlay_previous = share-y
show_data_range = false

[spacer]
height = 0.5

[hic matrix]
file = Li_et_al_2015.h5
title = depth = 250000; transform = log1p; colormap = bone_r (links: overlay_previous = share-y; links_type = triangles; color = darkred; line_style = dashed, bigwig: color = red)
colormap = bone_r
min_value = 15
max_value = 200
depth = 250000
transform = log1p
file_type = hic_matrix
show_masked_bins = false

[test arcs]
file = links2.links
title = 
links_type = triangles
line_style = dashed
overlay_previous = share-y
line_width = 0.8
color = darkred
show_data_range = false


[test bigwig]
file = bigwig2_X_2.5e6_3.5e6.bw
color = red
height = 4
title = 
overlay_previous = yes
min_value = 0
max_value = 50
show_data_range = false

[spacer]
height = 0.5

[hic matrix]
file = Li_et_al_2015.h5
title = depth = 200000; show_masked_bins = true; colormap = ['blue', 'yellow', 'red']; max_value = 150
depth = 200000
colormap = ['blue', 'yellow', 'red']
max_value = 150
file_type = hic_matrix
show_masked_bins = true

[spacer]
height = 0.1

[x-axis]

```

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

### Run PyGenomeTracks with BigWig, Genes, and Vlines

Source: https://pygenometracks.readthedocs.io/en/latest/content/examples

This command executes PyGenomeTracks with a configuration including bigwig, genes, and vertical lines, specifying a region and output file.

```bash
$ pyGenomeTracks --tracks bigwig_with_genes_and_vlines.ini --region X:2,800,000-3,100,000 -o bigwig_with_genes_and_vlines.png

```

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

### Run pyGenomeTracks for Epilogos Visualization

Source: https://pygenometracks.readthedocs.io/en/latest/content/examples

This command executes pyGenomeTracks to generate a PNG image of the epilogos track. It takes a track configuration file, a genomic region, and an output file name as input.

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

```

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

### Run PyGenomeTracks with Basic BigWig Track

Source: https://pygenometracks.readthedocs.io/en/latest/content/examples

This command executes PyGenomeTracks using a configuration file for a bigwig track, specifying a genomic region and an output file name.

```bash
$ pyGenomeTracks --tracks bigwig_track.ini --region X:2,500,000-3,000,000 -o bigwig.png

```

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

### Install pygenometracks with Mamba

Source: https://pygenometracks.readthedocs.io/en/latest/content/installation

Installs pyGenomeTracks using mamba for faster installations. It first creates a conda environment with mamba, then installs pygenometracks within that activated environment. Specific versions can also be installed.

```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

```

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

### Run pyGenomeTracks with Rasterization and Height Settings

Source: https://pygenometracks.readthedocs.io/en/latest/content/examples

Command-line execution of pyGenomeTracks using a configuration file that includes rasterization and height settings for Hi-C tracks. Specifies region, label fraction, width, DPI, and output file.

```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
```

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

### Install pygenometracks with Conda

Source: https://pygenometracks.readthedocs.io/en/latest/content/installation

Installs pyGenomeTracks and its dependencies using conda. It creates a new conda environment named 'pygenometracks'. You can specify a particular version of pygenometracks and python.

```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

```

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

### Plot MACS2 NarrowPeak Files with pyGenomeTracks

Source: https://pygenometracks.readthedocs.io/en/latest/content/examples

This example illustrates plotting peaks from MACS2 narrowPeak format using pyGenomeTracks. Various configuration options are shown, including height, max_value, line_width, show_labels, show_data_range, color, use_summit, and width_adjust. The output file visualizes peak start, end, summit, and height.

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

```

```ini
[narrow]
file = test2.narrowPeak
height = 4
max_value = 40
line_width = 0.1
title = max_value = 40;line_width = 0.1

[narrow 2]
file = test2.narrowPeak
height = 2
show_labels = false
show_data_range =  false
color = #00FF0080
use_summit = false
title = show_labels = false; show_data_range = false; use_summit = false; color = #00FF0080

[spacer]

[narrow 3]
file = test2.narrowPeak
height = 2
show_labels = false
color = #0000FF80
use_summit = false
width_adjust = 4
title = show_labels = false; use_summit = false; width_adjust = 4

[spacer]

[narrow 4]
file = test2.narrowPeak
height = 3
type = box
color = blue
line_width = 2
title = type = box; color = blue; line_width = 2

[spacer]

[narrow 5]
file = test2.narrowPeak
height = 3
type = box
color = blue
use_summit = false
title = type = box; color = blue; use_summit = false

[x-axis]

```

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

### BigWig Track with Gene Annotations and Vertical Lines

Source: https://pygenometracks.readthedocs.io/en/latest/content/examples

This configuration adds vertical lines from a BED file to the previous setup of bigwig and gene tracks. The 'type = vlines' setting enables vertical lines.

```ini
[bigwig file test]
file = bigwig.bw
# height of the track in cm (optional value)
height = 4
title = bigwig
min_value = 0
max_value = 30

[spacer]
# this simply adds an small space between the two tracks.

[genes]
file = genes.bed.gz
height = 7
title = genes
fontsize = 10
file_type = bed
gene_rows = 10

[x-axis]
fontsize=10

[vlines]
file = domains.bed
type = vlines

```

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

### pyGenomeTracks Bed Track Configuration Example

Source: https://pygenometracks.readthedocs.io/en/latest/content/tracks/bed

This configuration snippet demonstrates how to set up a 'bed' track in pyGenomeTracks. It includes essential parameters like 'title', 'height', and 'color', along with commented-out options for advanced customization such as 'orientation', 'overlay_previous', and color mapping based on BED file columns.

```text
# title of track (plotted on the right side)
title =
# height of track in cm (ignored if the track is overlay on top the previous track)
height = 2
# if you want to plot the track upside-down:
# orientation = inverted
# if you want to plot the track on top of the previous track. Options are 'yes' or 'share-y'.
# For the 'share-y' option the y axis values is shared between this plot and the overlay plot.
# Otherwise, each plot use its own scale
#overlay_previous = yes

# If the bed file contains a column for color (column 9), then this color can be used by
# setting:
#color = bed_rgb
# if color is a valid colormap name (like RbBlGn), then the score (column 5) is mapped
# to the colormap.
# In this case, the the min_value and max_value for the score can be provided, otherwise
# the maximum score and minimum score found are used.
#color = RdYlBu
#min_value=0
#max_value=100
# If the color is simply a color name, then this color is used and the score is not considered.
color = darkblue
# optional: line_width
#line_width = 0.5
# optional: border_color
# default is black.
# To remove the border, simply set 'border_color' to none
# Not used in tssarrow style
#border_color = black
# the display parameter defines how the bed file is plotted.
# Default is 'stacked' where regions are plotted on different lines so
# we can see all regions and all labels.
# The other options are ['collapsed', 'interleaved', 'triangles', 'squares', 'deletions', 'inversions']
# These 2 options assume that the regions do not overlap:
# `collapsed`: The bed regions are plotted one after the other in one line.
```

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

### MAF Track Configuration in pyGenomeTracks

Source: https://pygenometracks.readthedocs.io/en/latest/content/tracks/maf

This snippet shows how to configure a MAF track in pyGenomeTracks. It includes necessary parameters like 'file' and 'reference', and various optional parameters for customization such as title, height, colors, and species ordering. The example demonstrates a typical setup for visualizing multiple sequence alignments.

```python
# title of track (plotted on the right side)
title =
# height of track in cm (ignored if the track is overlay on top the previous track)
height = 2
# if you want to plot the track upside-down:
# orientation = inverted
# if you want to plot the track on top of the previous track. Options are 'yes' or 'share-y'.
# For the 'share-y' option the y axis values is shared between this plot and the overlay plot.
# Otherwise, each plot use its own scale
#overlay_previous = yes

# In addition to the maf file the reference genome is required:
# For example
#reference = mm10
# To speed the access to specific region
# The maf file needs an index.
# The default is the file
# followed by '.index'. Alternatively another
# file can be specified.
# If it does not exists it will be created:
#file_index = 
# Set colors
#color_identical = black
#color_mismatch = grey
#color_gap = lightgrey
# Set line_width
#line_width = 0.5
# optional: the species order
#species_order = hg18 panTro2
# optional if species_order is specified (don't use space in names)
#species_labels = human chimpanzee
# optional if species_order is specified and they are the only one you want:
#species_order_only = true
# optional if you want to see the DNA sequence of the ref
#display_ref_seq = true
# You can choose to rasterize the block part of the maf by using:
#rasterize = true
# optional: If not given is guessed from the file ending.
file_type = maf
    
```

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

### PyGenomeTracks: Command to generate BED tracks visualization with arrowheads

Source: https://pygenometracks.readthedocs.io/en/latest/content/examples

This command runs PyGenomeTracks using a configuration file focused on BED tracks and their arrowhead display options. It specifies the region, track label fraction, image dimensions, and output file.

```bash
$ pyGenomeTracks --tracks bed_arrow_tracks.ini --region X:3130000-3140000 --trackLabelFraction 0.2 --width 38 --dpi 130 -o master_bed_arrow_zoom.png

```

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

### Configure Epilogos Track with pyGenomeTracks

Source: https://pygenometracks.readthedocs.io/en/latest/content/examples

This configuration defines an epilogos track for pyGenomeTracks. It requires a qcat file and can optionally include a title and categories file for custom coloring. The output is an image file showing the epilogos visualization.

```ini
[epilogos]
file = epilog.qcat.bgz
height = 5
title = height=5; categories_file=epilog_cats.json

[x-axis]

```
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