Plotting CapCruncher output¶

Introduction¶

This is a quick overview of the plotting functionality of CapCruncher. Please ensure that you have installed the optional dependencies for CapCruncher by running:

pip install capcruncher[full]

Imports¶

In [1]:

import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import coolbox.api as cb
from capcruncher.api.plotting import CCTrack, CCFigure
import pyranges as pr

import pandas as pd import numpy as np import matplotlib.pyplot as plt import coolbox.api as cb from capcruncher.api.plotting import CCTrack, CCFigure import pyranges as pr

Read plotting coordinates¶

In [2]:

viewpoints = pr.read_bed("alpha_tile_mm9.bed")
viewpoints

viewpoints = pr.read_bed("alpha_tile_mm9.bed") viewpoints

Out[2]:

	Chromosome	Start	End	Name
0	chr11	29902950	33226736	Alpha

Plot using the CapCruncher API¶

First create a number of CCTrack instances supported track types:

• heatmap - a contact matrix heatmap in cool format
• bigwig - a bigwig file containing the number of reads per bin
• bigwig_summary - a collection of bigwig files containing the number of reads per bin
• scale - a scale bar. Does not require a file to be specified
• bed - a bed file
• xaxis - an x-axis of genomic coordinates. Does not require a file to be specified
• genes - a gene track in bed12 format
• spacer - a spacer track. Does not require a file to be specified

Create new CCTrack objects¶

Option 1: Create a list of CCTrack objects and pass them to CCFigure¶

In [3]:

tracks = [
    CCTrack(None, type="scale"),
    CCTrack(
        "capcruncher_output/results/WT_FL_S3_Replicate1/WT_FL_S3_Replicate1.hdf5",
        type="heatmap",
        binsize=2000,
        title="Alpha Tile",
        viewpoint="Alpha",
        normalization="ice",
        transform="yes",
        style="triangular",
    ),
    CCTrack(None, type="spacer"),
    CCTrack(None, type="spacer"),
    CCTrack(None, type="xaxis"),
]

fig = CCFigure(tracks, auto_spacing=False)

tracks = [ CCTrack(None, type="scale"), CCTrack( "capcruncher_output/results/WT_FL_S3_Replicate1/WT_FL_S3_Replicate1.hdf5", type="heatmap", binsize=2000, title="Alpha Tile", viewpoint="Alpha", normalization="ice", transform="yes", style="triangular", ), CCTrack(None, type="spacer"), CCTrack(None, type="spacer"), CCTrack(None, type="xaxis"), ] fig = CCFigure(tracks, auto_spacing=False)

Option 2: Create a CCFigure object and add tracks to it¶

As this would overwrite the previous figure, we will create a new figure and add the tracks to it.

In [4]:

fig2 = CCFigure(tracks, auto_spacing=False)
fig2.add_track(CCTrack(None, type="scale"))

fig2 = CCFigure(tracks, auto_spacing=False) fig2.add_track(CCTrack(None, type="scale"))

Plot the figure (Optional)¶

In [5]:

# Plot a specific region if desired
fig.plot("chr11:29902950-33226736")

# Plot a specific region if desired fig.plot("chr11:29902950-33226736")

Out[5]:

Save the figure¶

Two options:

1. Save the figure as a static image using the save method of the CCFigure.
2. Save the CCFigure as a TOML file which can be edited and either reloaded into a CCFigure or used by the command line interface to generate a new figure using capcruncher plot make-plot.

Option 1: Save the figure to a file¶

In [6]:

fig.save("chr11:29902950-33226736", output="test.png")

fig.save("chr11:29902950-33226736", output="test.png")

Option 2: Save the figure as a template¶

In [7]:

fig.to_toml(output="template.toml")

fig.to_toml(output="template.toml")

This will look something like this:

In [21]:

!head -n 15 template.toml

!head -n 15 template.toml

["scale 0"]
type = "scale"

["spacer 0"]
type = "spacer"

["spacer 1"]
type = "spacer"

["Alpha Tile"]
type = "heatmap"
binsize = 2000
title = "Alpha Tile"
viewpoint = "Alpha"
normalization = "ice"

This template can be re-loaded using the CapCruncher package e.g. using the CCFigure.from_toml method. You can also add new tracks to the figure and re-plot it.

See this rather contrived example of reloading the figure and adding a new scale bar to it.

In [14]:

fig = CCFigure.from_toml("template.toml")
fig.add_track(CCTrack(None, type="scale"))
fig.plot("chr11:29902950-33226736")

fig = CCFigure.from_toml("template.toml") fig.add_track(CCTrack(None, type="scale")) fig.plot("chr11:29902950-33226736")

Out[14]:

Alternatively the template can be edited and used on the commandline with capcruncher plot e.g.

In [18]:

%%bash
capcruncher \
plot \
--template template.toml \
--region chr11:29902950-33226736 \
-o test.png

%%bash capcruncher \ plot \ --template template.toml \ --region chr11:29902950-33226736 \ -o test.png

This will generate the same figure as before: