pycallingcards.plotting.WashU_browser_url#

pycallingcards.plotting.WashU_browser_url(qbed={}, bed={}, genome='hg38', dirc='WashU_cache', remove=False)[source]#

Display qbed, bed data in WashU Epigenome Browser [Li et al., 2019].

Parameters:

  • qbed (dict (default: {})) – A dictionary for input qbed data key as the name to display and value is the path or data of the file. Prefer path.

  • bed (dict (default: {})) – A dictionary for input bed data(peak data) key as the name to display and value is the path or data of the file. Prefer path.

  • genome (Optional[Literal['hg38', 'mm10', 'sacCer3']] (default: 'hg38')) – Genome to display. Currently, ‘hg38’, ‘mm10’, ‘sacCer3’ are provided only.

  • dirc (str (default: 'WashU_cache')) – The directory for all the cache files.

  • remove (bool (default: False)) – Weather to remove the directory or not.

Example:

>>> import pycallingcards as cc
>>> SP1_P10 = cc.datasets.SP1_Cre_data(data="SP1_P10")
>>> SP1_P28 = cc.datasets.SP1_Cre_data(data="SP1_P28")
>>> cc.rd.combine_qbed([SP1_P10,SP1_P28])
>>> peak_data = cc.pp.callpeaks(SP1,  method = "CCcaller", reference = "mm10", pvalue_cutoffbg = 0.1, maxbetween = 1800,
              pvalue_cutoffTTAA = 0.001, lam_win_size = None,  pseudocounts = 0.1, record = True, save = "peak1.bed")
>>> qbed = {"SP1":SP1}
>>> bed = {'PEAK1':peak_data}
>>> cc.pl.WashU_browser_url(qbed,bed,genome = "mm10")