#NEWLINE# def __init__( self , ip , control , db = None , peaks = None , local_coverage_kwargs = dict ( stranded = False ) , ip_style = None , control_style = None , peaks_style = None , max_bins = 500 ) : #NEWLINE# #INDENT# '\n        Mini-browser to show IP and control signal, along with optional peaks\n        and gene models.  See module-level documentation for details.\n\n        Parameters\n        ----------\n        ip, control : genomic_signal object\n            These can be any kind of genomic signal object.  If BamSignal, then\n            the signal will be scaled by million mapped reads.\n\n        db : filename or gffutils.FeatureDB\n            Optional database of annotations.  If provided, gene models will be\n            plotted on an additional axes.\n\n        peaks : filename or pybedtools.BedTool object\n            Optional file of called peaks.  If provided, will be plotted on an\n            additional axes.\n\n        local_coverage_kwargs : dict\n            Kwargs to pass on to the local_coverage method of `ip` and\n            `control`.  It is recommended that at least `stranded=False` is\n            included, since the mini-browser always displays the plus strand.\n\n        ip_style, control_style : dict\n            Kwargs to pass to Axes.fill_between (e.g. colors, alpha, line\n            styles)\n\n        peaks_style : dict\n            Kwargs to pass to PolyCollection (e.g., face_color, edgewidth)\n\n        max_bins : int\n            Maximum number of bins to use when getting genomic_signal.  This\n            can be overridden by providing the `bins` kwarg in\n            `local_coverage_kwargs`.\n\n        Notes\n        -----\n        After creation, settings can be changed in between calls to the\n        `plot()` method.\n\n        For example, the self.settings dictionary, which\n        contains arguments passed to the gffutils.contrib.plotting.Gene class,\n        can be modified to specify which kinds of features should be plotted.\n        The `gs` attribute contains the matplotlib.gridspec.GridSpec object,\n        which can be used to modify the relative sizes of the subplots.\n\n\n        ' #NEWLINE# super ( ChIPSeqMiniBrowser , self ) . __init__ ( [ ip , control ] ) #NEWLINE# self . local_coverage_kwargs = ( local_coverage_kwargs or { #NEWLINE# #INDENT# #NEWLINE# #UNINDENT# } ) #NEWLINE# self . ip = ip #NEWLINE# self . control = control #NEWLINE# if isinstance ( db , basestring ) : #NEWLINE# #INDENT# db = gffutils . FeatureDB ( db ) #NEWLINE# #UNINDENT# self . db = db #NEWLINE# self . ip_style = ( ip_style or { #NEWLINE# #INDENT# #NEWLINE# #UNINDENT# } ) #NEWLINE# self . peaks_style = ( peaks_style or { #NEWLINE# #INDENT# #NEWLINE# #UNINDENT# } ) #NEWLINE# self . control_style = ( control_style or { #NEWLINE# #INDENT# #NEWLINE# #UNINDENT# } ) #NEWLINE# if ( peaks is not None ) : #NEWLINE# #INDENT# peaks = pybedtools . BedTool ( peaks ) #NEWLINE# #UNINDENT# self . peaks = peaks #NEWLINE# self . max_bins = max_bins #NEWLINE# self . settings = { #NEWLINE# #INDENT# 'transcripts' : None , #NEWLINE# 'cds' : [ 'CDS' ] , #NEWLINE# 'utrs' : [ 'exon' ] , #NEWLINE# 'color' : '0.5' , #NEWLINE# 'featuretype' : 'gene' , #NEWLINE# #UNINDENT# }