def r_igraph_clust_coeff(g, save_fn=None):
"""
Compute clustering coefficient/transitivity of graph g
and save as necessary
@param g: The igraph loaded via Rpy2 so an R object
@param save_fn: the filename you want to use to save it. If not provided
the graph adds a clustcoeff attribute to all nodes and returns.
@return: the graph with the clustcoeff attribute appended
"""
clustcoeff = robjects.r("""
suppressMessages(require(igraph))
fn <- function(g){
igraph::transitivity(g, "local")
}
""")
ccvector = clustcoeff(g)
if save_fn:
save_fn = os.path.abspath(save_fn)
createSave(save_fn, ccvector) # TODO: Clean input for programmatic access
print "Clustering Coefficient saved as %s ..." % save_fn
else:
g = r_igraph_set_vertex_attr(g, "clustcoeff", ccvector) # Attribute name may need to change
return g # return so we can use for other attributes
def r_igraph_clust_coeff(g, save_fn=None):
"""
Compute clustering coefficient/transitivity of graph g
and save as necessary
@param g: The igraph loaded via Rpy2 so an R object
@param save_fn: the filename you want to use to save it. If not provided
the graph adds a clustcoeff attribute to all nodes and returns.
@return: the graph with the clustcoeff attribute appended
"""
clustcoeff = robjects.r("""
suppressMessages(require(igraph))
fn <- function(g){
igraph::transitivity(g, "local")
}
""")
ccvector = clustcoeff(g)
if save_fn:
save_fn = os.path.abspath(save_fn)
createSave(save_fn,
ccvector) # TODO: Clean input for programmatic access
print "Clustering Coefficient saved as %s ..." % save_fn
else:
g = r_igraph_set_vertex_attr(
g, "clustcoeff", ccvector) # Attribute name may need to change
return g # return so we can use for other attributes
def r_igraph_scan1(g, save_fn=None):
"""
Compute the scan statistic 1 of graph g and save as necessary
@param g: The igraph loaded via Rpy2 so an R object
@param save_fn: the filename you want to use to save it. If not provided
the graph adds a scan1 attribute to all nodes and returns.
@return: The graph with the scan1 attribute appended
"""
scanstat1 = robjects.r("""
suppressMessages(require(igraph))
fn <- function(g){
igraph::local_scan(g)
}
""")
ss1vector = scanstat1(g)
if save_fn:
save_fn = os.path.abspath(save_fn)
createSave(os.path.abspath(save_fn),
ss1vector) # TODO: Clean input for programmatic access
print "Scan Statistic saved as %s ..." % save_fn
else:
g = r_igraph_set_vertex_attr(
g, "scan1", ss1vector) # Attribute name may need to change
return g # return so we can use for other attributes
def r_igraph_triangles(g, save_fn=None):
"""
Compute local triangle count of graph g and save as necessary
@param g: The igraph loaded via Rpy2 so an R object
@param save_fn: the filename you want to use to save it. If not provided
the graph adds a tri count attribute to all nodes and returns.
@return: The graph with the tri vertex attribute appended
"""
triangles = robjects.r("""
suppressMessages(require(igraph))
fn <- function(g){
igraph::adjacent.triangles(g)
}
""")
trivector = triangles(g)
if save_fn:
save_fn = os.path.abspath(save_fn)
createSave(save_fn,
trivector) # TODO: Clean input for programmatic access
print "Triangle Count saved as %s ..." % save_fn
else:
g = r_igraph_set_vertex_attr(
g, "tri", trivector) # Attribute name may need to change
return g # return so we can use for other attributes
def r_igraph_degree(g, mode="total", save_fn=None):
"""
Compute degree of graph g and save as necessary
@param g: The igraph loaded via Rpy2 so an R object
@param mode: the type of degree. Default is an undirected i.e. in-degree + out degree
@param save_fn: the filename you want to use to save it. If not provided
the graph adds a degree attribute to all nodes and returns.
@return: the graph with the degree attribute set.
"""
deg = robjects.r("""
suppressMessages(require(igraph))
fn <- function(g){
igraph::degree(g, mode="%s")
}
""" % mode)
degvector = deg(g)
if save_fn:
save_fn = os.path.abspath(save_fn)
createSave(save_fn,
degvector) # TODO: Clean input for programmatic access
print "Degree saved as %s ..." % save_fn
else:
g = r_igraph_set_vertex_attr(
g, "degree", degvector) # Attribute name may need to change
return g # return so we can use for other attributes
def r_igraph_degree(g, mode="total", save_fn=None):
"""
Compute degree of graph g and save as necessary
@param g: The igraph loaded via Rpy2 so an R object
@param mode: the type of degree. Default is an undirected i.e. in-degree + out degree
@param save_fn: the filename you want to use to save it. If not provided
the graph adds a degree attribute to all nodes and returns.
@return: the graph with the degree attribute set.
"""
deg = robjects.r(
"""
suppressMessages(require(igraph))
fn <- function(g){
igraph::degree(g, mode="%s")
}
"""
% mode
)
degvector = deg(g)
if save_fn:
save_fn = os.path.abspath(save_fn)
createSave(save_fn, degvector) # TODO: Clean input for programmatic access
print "Degree saved as %s ..." % save_fn
else:
g = r_igraph_set_vertex_attr(g, "degree", degvector) # Attribute name may need to change
return g # return so we can use for other attributes
def r_igraph_triangles(g, save_fn=None):
"""
Compute local triangle count of graph g and save as necessary
@param g: The igraph loaded via Rpy2 so an R object
@param save_fn: the filename you want to use to save it. If not provided
the graph adds a tri count attribute to all nodes and returns.
@return: The graph with the tri vertex attribute appended
"""
triangles = robjects.r("""
suppressMessages(require(igraph))
fn <- function(g){
igraph::adjacent.triangles(g)
}
""")
trivector = triangles(g)
if save_fn:
save_fn = os.path.abspath(save_fn)
createSave(save_fn, trivector) # TODO: Clean input for programmatic access
print "Triangle Count saved as %s ..." % save_fn
else:
g = r_igraph_set_vertex_attr(g, "tri", trivector) # Attribute name may need to change
return g # return so we can use for other attributes
def r_igraph_scan1(g, save_fn=None):
"""
Compute the scan statistic 1 of graph g and save as necessary
@param g: The igraph loaded via Rpy2 so an R object
@param save_fn: the filename you want to use to save it. If not provided
the graph adds a scan1 attribute to all nodes and returns.
@return: The graph with the scan1 attribute appended
"""
scanstat1 = robjects.r("""
suppressMessages(require(igraph))
fn <- function(g){
igraph::local_scan(g)
}
""")
ss1vector = scanstat1(g)
if save_fn:
save_fn = os.path.abspath(save_fn)
createSave(os.path.abspath(save_fn), ss1vector) # TODO: Clean input for programmatic access
print "Scan Statistic saved as %s ..." % save_fn
else:
g = r_igraph_set_vertex_attr(g, "scan1", ss1vector) # Attribute name may need to change
return g # return so we can use for other attributes
print "eigenvectors ssaved as %s ..." % save_fn[1]
else:
global gl_eigvects
gl_eigvects = eigs[0][1]
print "Setting eigenvalues as graph attr ..."
g = r_igraph_set_graph_attribute(g, "eigvals", "["+", ".join(map(cut, (eigs[0][0])))+"]") # Return a comma separated string
eig_idx = eigs[1]
print "Mapping eigenvectors ..."
eigvects = map(get_str_eigvects, [(idx, idx+nev) for idx in xrange(0, ((len(eigs[1]))*nev), nev)])
del eigs
print "Setting eigenvectors as vertex attr ..."
g = r_igraph_set_vertex_attr(g, "latent_pos", value=eigvects, index=eig_idx, is_str=True) # Could not create char sequences only lists :-/
print "Eigenvalue computation not saved to disk. Eigen-pairs added as graph attributes ...."
return g
def get_str_eigvects(idx):
"""
Used for mapping to get eigenvectors that correspond to each vertex of the graph
@param idx: a 2-tuple that gives the indexes of the eigenvector 1-d flattened matrix that correspond
to the particular vertex
@return: A vector i.e the eigenvector (latent position) for that vertex cast to a string
"""
global gl_eigvects
return "["+", ".join(map(cut, (gl_eigvects[idx[0]:idx[1]])))+"]"
print "Setting eigenvalues as graph attr ..."
g = r_igraph_set_graph_attribute(
g, "eigvals", "[" + ", ".join(map(cut, (eigs[0][0]))) +
"]") # Return a comma separated string
eig_idx = eigs[1]
print "Mapping eigenvectors ..."
eigvects = map(get_str_eigvects,
[(idx, idx + nev)
for idx in xrange(0, ((len(eigs[1])) * nev), nev)])
del eigs
print "Setting eigenvectors as vertex attr ..."
g = r_igraph_set_vertex_attr(
g, "latent_pos", value=eigvects, index=eig_idx,
is_str=True) # Could not create char sequences only lists :-/
print "Eigenvalue computation not saved to disk. Eigen-pairs added as graph attributes ...."
return g
def get_str_eigvects(idx):
"""
Used for mapping to get eigenvectors that correspond to each vertex of the graph
@param idx: a 2-tuple that gives the indexes of the eigenvector 1-d flattened matrix that correspond
to the particular vertex
@return: A vector i.e the eigenvector (latent position) for that vertex cast to a string
"""
