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IMP Reference Guide  develop.cc86c9801d,2022/11/22
The Integrative Modeling Platform
IMP.pmi.plotting.topology.TopologyPlot Class Reference

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

Inherits object.

Detailed Description

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

Note
This class is only available in Python.

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
modelThe IMP model
selection_dictA dictionary containing component names. Keys are labels values are either moleculename or start,stop,moleculename
cutoffThe distance cutoff
frequency_cutoffThe frequency cutoff
colorsA dictionary of colors (HEX code,values) for subunits (keywords)
fixedA list of subunits that are kept fixed
posA dictionary with positions (tuple, values) of subunits (keywords)
proteomic_edgesA list edges to represent proteomic data
quantitative_proteomic_dataA dictionary of edges to represent quantitative proteomic data such as PE Scores, or genetic interactions

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

Member Function Documentation

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

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


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