Detailed Description

A class to read RMF files and make a network contact map.

Definition at line 12 of file plotting/topology.py.

Public Member Functions
def	__init__
	Set up a new graphXL object. More...

def	add_rmf
	Add selections from an RMF file. More...

def	make_plot
	plot the interaction matrix More...

Constructor & Destructor Documentation

def IMP.pmi.plotting.topology.TopologyPlot.__init__	(	self,
		model,
		selections,
		cutoff,
		frequency_cutoff,
		colors = `None`,
		fixed = `None`,
		pos = `None`,
		proteomic_edges = `None`,
		quantitative_proteomic_data = `None`
	)

Set up a new graphXL object.

Parameters

model	The IMP model
selection_dict	A dictionary containing component names. Keys are labels values are either moleculename or start,stop,moleculename
cutoff	The distance cutoff
frequency_cutoff	The frequency cutoff
colors	A dictionary of colors (HEX code,values) for subunits (keywords)
fixed	A list of subunits that are kept fixed
pos	A dictionary with positions (tuple, values) of subunits (keywords)
proteomic_edges	A list edges to represent proteomic data
quantitative_proteomic_data	A dictionary of edges to represent quantitative proteomic data such as PE Scores, or genetic interactions

Definition at line 30 of file plotting/topology.py.

def IMP.pmi.plotting.topology.TopologyPlot.add_rmf	(	self,
		rmf_fn,
		nframe
	)

Add selections from an RMF file.

Definition at line 56 of file plotting/topology.py.

def IMP.pmi.plotting.topology.TopologyPlot.make_plot	(	self,
		groups,
		out_fn,
		quantitative_proteomic_data = `False`
	)

plot the interaction matrix

Parameters

groups	is the list of groups of domains, eg, [["protA_1-10","prot1A_11-100"],["protB"]....] it will plot a space between different groups
out_fn	name of the plot file
quantitative_proteomic_data	plot the quantitative proteomic data

Definition at line 103 of file plotting/topology.py.

The documentation for this class was generated from the following file: