Example #1
0
#!/usr/bin/env python-i
# example of using summatrix from within python

# load summon matrix library
from summon import matrix

# read in matrix (stored in Index Format 'imat')
mat = matrix.Matrix()
matrix.open_matrix("human_mouse.imat", mat, format="imat")

# create and show matrix viewer
viewer = matrix.MatrixViewer(mat, title="human vs mouse")
viewer.show()

Example #2
0
                if row not in mat: mat[row] = {}
                mat[row][col] = val
                if symmetrize:
                    if col not in mat: mat[col] = {}
                    mat[col][row] = val
    ff.close()
    return nnodes, nedges


infile, mtype, size, view = parse_arguments(sys.argv[1:])

from summon import matrix

if mtype == "hmat":
    mat = matrix.Matrix()
    matrix.open_matrix(infile, mat, format=mtype, symmetrize=True)
else:
    mat = {}
    nnodes, nedges = my_open_matrix(infile, mat, mtype, True)

mini = minj = maxi = maxj = 1
for i, cols in mat.iteritems():
    maxi = max(maxi, i)
    mini = min(mini, i)
    for j, val in cols.iteritems():
        maxj = max(maxj, j)
        minj = min(minj, j)
maxy = maxx = max(maxi, maxj)

print mini, minj, maxi, maxj
if size == 0: size = maxx
Example #3
0
#!/usr/bin/env python-i
# example of using summatrix from within python

# load summon matrix library
from summon import matrix

# read in matrix (stored in Compressed Row Format 'rmat')
mat = matrix.Matrix()
matrix.open_matrix("dog_human.mat", mat, format="rmat")

# create and show matrix viewer
viewer = matrix.MatrixViewer(mat, title="dog vs human")
viewer.show()

Example #4
0
#!/usr/bin/env python-i
# use summatrix to visualize a dense matrix
#

# load summon matrix library
import summon
from summon import matrix, util



# read in matrix (stored in Index Format 'imat')
mat = matrix.Matrix()
matrix.open_matrix("data.mat", mat, format="dmat")

# set colormap
mat.colormap = summon.PosNegColorMap()

# read row and column labels
mat.rowlabels = util.read_strings("data.rlabels")
mat.collabels = util.read_strings("data.clabels")


# create and show matrix viewer
viewer = matrix.MatrixViewer(mat, title="unclustered data",
                             show_labels=True,
                             bgcolor=(1,1,1),
                             style="quads",
                             winsize=(400, 600))
viewer.show()

Example #5
0
				if row not in mat: mat[row] = {}
				mat[row][col] = val
				if symmetrize:
					if col not in mat: mat[col] = {}
					mat[col][row] = val
	ff.close()
	return nnodes, nedges


infile, mtype, size, view = parse_arguments(sys.argv[1:])

from summon import matrix

if mtype == "hmat":
	mat = matrix.Matrix()
	matrix.open_matrix(infile, mat, format = mtype, symmetrize = True)
else:
	mat = {}
	nnodes, nedges = my_open_matrix(infile, mat, mtype, True)

mini = minj = maxi = maxj = 1
for i, cols in mat.iteritems():
	maxi = max(maxi, i)
	mini = min(mini, i)	
	for j, val in cols.iteritems():
		maxj = max(maxj, j)
		minj = min(minj, j)
maxy = maxx = max(maxi, maxj)

print mini, minj, maxi, maxj
if size == 0: size = maxx
# example of using summatrix from within python
# view a matrix in label format

print
print "NOTE: try quering matrix values using the following syntax:"
print "  mat['human']['Cow']"
print


# load summon matrix library
import summon
from summon import matrix

# read in matrix (stored in Labeled Format 'limat')
mat = matrix.Matrix()
mat.order = "mammals_distances.labels"  # set the labels needed for matrix
matrix.open_matrix("mammals_distances.lmat", mat, format="lmat")

# read color map for matrix
mat.colormap = summon.read_color_map("mammals_distances.colormap")

# create and show matrix viewer
viewer = matrix.MatrixViewer(mat, title="Mammals distances",
                             bgcolor=(1,1,1),  # use white background (r,g,b)
                             style="quads",    # use squares for matrix entries
                             show_labels=True, # show labels
                             show_label_windows=True) # use a separate window
                                                      # for labels
viewer.show()