def setup(self, nrows=None, ncols=None, nnz=None,
rowsample=False, colsample=False):
# set dimensions
if nrows is not None:
self.nrows = nrows
if ncols is not None:
self.ncols = ncols
if nnz is not None:
self.nnz = nnz
# set permutations
if self.rperm is None:
self.rperm = range(self.nrows)
if self.cperm is None:
self.cperm = range(self.ncols)
# set inverse permutations
self.rinv = util.invperm(self.rperm)
self.cinv = util.invperm(self.cperm)
# setup row/col sampling
if rowsample is not False:
self.rshow = set(random.sample(range(self.nrows),
int(self.nrows * rowsample)))
else:
self.rshow = set(range(self.nrows))
if colsample is not False:
self.cshow = random.sample(range(self.ncols),
int(self.ncols * colsample))
else:
self.cshow = set(range(self.ncols))
def set_perm_from_part(mat, rows=True, cols=True):
# setup default permutation from cluster ids
if rows and mat.rpart:
mat.rperm = part2perm(mat.rpart)
mat.rinv = util.invperm(mat.rperm)
if cols and mat.cpart:
mat.cperm = part2perm(mat.cpart)
mat.cinv = util.invperm(mat.cperm)
def __init__(self, mat=None, on_click=None,
bgcolor=(0,0,0), drawzeros=False, style="points",
show_labels=False, show_label_windows=False,
winsize=(400,400), title="summatrix",
rtree=None, ctree=None,
use_tree_lens=(False, False),
show_tree_windows=None):
self.win = None
self.mat = mat
self.bgcolor = bgcolor
self.drawzeros = drawzeros
self.style = style
self.winsize = winsize[:]
self.title = title
self.part_lines = None
self.part_lines_visible = True
self.first_open = True
if on_click != None:
self.on_click = on_click
# labels
self.show_labels = show_labels
self.show_label_windows = show_label_windows
self.label_windows = [None, None]
# trees
if show_tree_windows != False and (rtree != None or ctree != None):
self.show_tree_windows = True
else:
self.show_tree_windows = False
self.tree_windows = [None, None]
self.rtree = rtree
self.ctree = ctree
self.use_tree_lens = use_tree_lens
# setup perm based on trees
if self.rtree:
leaves = self.rtree.leaf_names()
if self.mat.rowlabels == None:
self.mat.rperm = map(int, leaves)
else:
lookup = util.list2lookup(self.mat.rowlabels)
self.mat.rperm = util.mget(lookup, leaves)
if self.ctree:
leaves = self.ctree.leaf_names()
if self.mat.collabels == None:
self.mat.cperm = map(int, leaves)
else:
lookup = util.list2lookup(self.mat.collabels)
self.mat.cperm = util.mget(lookup, leaves)
# set inverse permutations
self.mat.rinv = util.invperm(self.mat.rperm)
self.mat.cinv = util.invperm(self.mat.cperm)
def submatrix(self, rows=None, cols=None):
"""Returns a submatrix"""
mat = Matrix()
if rows == None:
rows = range(mat.nrows)
if cols == None:
cols = range(mat.ncols)
lookuprows = util.list2lookup(rows)
lookupcols = util.list2lookup(cols)
# get subset of data
rows2, cols2, vals2 = self.rows, self.cols, self.vals
rows3, cols3, vals3 = mat.rows, mat.cols, mat.vals
for i in xrange(len(rows2)):
r = rows2[i]
c = cols2[i]
v = vals2[i]
if r not in lookuprows or c not in lookupcols:
continue
r2 = lookuprows[r]
c2 = lookupcols[r]
rows3.append(r2)
cols3.append(c2)
vals3.append(v)
mat[r2][c2] = v
# get subset of permutation
ind = [self.rinv[i] for i in rows]
lookup = util.list2lookup(util.sort(ind))
mat.rinv = util.mget(lookup, ind)
mat.rperm = util.invperm(mat.rinv)
ind = [self.cinv[i] for i in cols]
lookup = util.list2lookup(util.sort(ind))
mat.cinv = util.mget(lookup, ind)
mat.cperm = util.invperm(mat.cinv)
# get subset of partition
if mat.rpart != None:
mat.rpart = util.mget(self.rpart, rows)
if mat.cpart != None:
mat.cpart = util.mget(self.cpart, cols)
mat.setup(len(rows), len(cols), len(rows3))
return mat