pycallingcards.plotting.whole_peaks#

pycallingcards.plotting.whole_peaks(peak_data, reference='mm10', figsize=(100, 50), title='Peaks over chromosomes', font_size=10, linewidth=4, color='black', added=10000, height_name='Experiment Insertions', height_scale=1.01, exact=False, save=False)[source]#

Plot all the peaks in chromosomes.

Parameters:

  • peak_data (DataFrame) – Peak_data file from cc.pp.callpeaks.

  • reference (default: 'mm10') – [‘mm10’,’hg38’,’sacCer3’,None]. The reference of the data.

  • figsize (Tuple[int, int] (default: (100, 50))) – The size of the figure.

  • title (str (default: 'Peaks over chromosomes')) – The title of the plot.

  • font_size (int (default: 10)) – The font of the words on the plot.

  • linewidth (float (default: 4)) – The linewidth between words on the plot.

  • color (str (default: 'black')) – The color of the plot, the same as color in plt.plot.

  • added (int (default: 10000)) – Only valid when there is no reference provided. The max length(bp) added to the end of a chromosome shown.

  • height_name (str (default: 'Experiment Insertions')) – The height of each peak. If None, it will all be the same height.

  • height_scale (float (default: 1.01)) – The relative height for the chromosome section of the tallest peak.

  • exact (bool (default: False)) – Wheather to show the exact number of total bp at the end of chromosome.

  • save (Union[bool, str] (default: False)) – Could be bool or str indicating the file name It will be saved. If True, a default name will be given and the plot would be saved as a png file.

Example:

>>> import pycallingcards as cc
>>> qbed_data = cc.datasets.mousecortex_data(data="qbed")
>>> peak_data = cc.pp.callpeaks(qbed_data, method = "CCcaller", reference = "mm10", record = True)
>>> cc.pl.whole_peaks(peak_data)