def plot_grid(fig, params):
grid =map(lambda x: x.strip().split(' '),
open(au.data_filepath(params['fname'])).readlines())
grid_rs = zeros((len(grid),len(grid[0])),int) + 200
if params['command'] == 'DumpLineageGrid':
grid =array(grid, float)
grid_colors = zeros(shape(grid),int)
grid_colors += grid
cols = ['Mut-Averse','Mut-Prone']
plotLinCounts(grid)
elif params['command'] == 'DumpTaskGrid':
grid_int = array(grid,int)
grid_colors = zeros(shape(grid_int),int) -1
while 1:
nz =nonzero(greater(grid_int,0))
if len(nz[0]) == 0 : break
grid_colors[nz[0],nz[1]]+= 1
grid_int /= 2
grid = grid_colors #(array(grid, float))
cols,data = au.parse_printed('tasks.dat')
cols = cols[1:]
elif params['command'] == 'PrintResourceData':
grid_int = array(grid,int)
grid_colors = grid_int
cols = [str(i) for i in range(max(grid_int)+1)]
else:
raise Exception('Grid type not implemented')
#grid = params['grid']
x = shape(grid)[0]
y = shape(grid)[1]
n = x * y
if x != y:
print "Grid not square, skipping"
return
fig.clear()
ct = mycolors.getct(len(cols))
nc = len(ct)
xs,ys,rs,cs = [[] for i in range(4)]
c_lambda = lambda x: x>=0 and ct[x] or [0,0,0]
arr = zeros((x,y,3))
for i in range(nc):
arr[nonzero(equal(grid, i))] = ct[i]
#for i in range(x):
# for j in range(y):
# grid_colors
#
#for i in range(x):
# for j in range(y):
# xs.append(i)
# ys.append(j)
# rs.append(grid_rs[i,j])
# cs.append(c_lambda( grid_colors[i,j]))
#ax = fig.add_subplot(111)
#ax.scatter(xs,ys,rs,cs)
plt.imshow(arr)
up.color_legend(fig,ct,cols)
plt.draw()
f.clear()
ax = f.add_axes([0,0,1,1])
ng = len(grids)
do_fold = False
if fold_grid and ng > 9:
do_fold = True
if do_fold:
grids2= grids[ng/2:]
grids = grids[0:ng/2]
ng /=2
ct = mycolors.getct(ng)
nx = ceil(sqrt(ng))
ny = ceil(sqrt(ng))
sx,sy = shape(grids[0])
m0 = np.max(grids)
if m0 == 0: m0 = 1
if do_fold: m1 = np.max(grids2)
if do_fold:
if m1 == 0: m1 = 1
margin = 3
if do_fold:
big_grid = zeros((nx*sx +(nx +1)* margin, ny * sy + (ny +1) * margin,3))
def plot_ts(fig,params,
do_grid_resources = True):
fname = params['fname']
window = params.get('window',20)
cols, data = au.parse_printed( fname)
data_dict_unfiltered = {}
widths_dict = {}
for i in range(len(cols)):
c = cols[i]
data_dict_unfiltered[c] = array(map(lambda x: x[i], data),float)
widths_dict[c] = i +1
if 'Update' in cols:
cols.remove('Update')
data_dict = {}
for c in cols:
data_dict[c] = data_dict_unfiltered[c]
name = params['name']
if name in ['tasks','fitness','all','cdata','res']:
pass
else:
raise Exception('unhandled graph type: '+name)
nplots = len(cols)
fig.clear()
widths = params.get('widths',1)
last_y = zeros(window)
ct =mycolors.getct(len(cols))
do_fold = False
if fold_ts and nplots > 9:
do_fold = True
if do_fold:
all_cols = [cols[0:nplots/2],cols[nplots/2:]]
else: all_cols = [cols]
j = 0
colors = ct[(nplots/len(all_cols)*j):(nplots/len(all_cols)*(j+1))]
yvals = zeros( (len(all_cols[j]) ,window ) )
for i in range(len(all_cols[j])):
c = all_cols[j][i]
n = min(window, len(data_dict[c]))
y_sm = data_dict[c][-n:]
yvals[i,-n:] = y_sm
seismic(fig, yvals, colors, cols)
up.color_legend(fig, colors, cols,pos = 3)
print 'Current level: ', cols[0], data_dict[cols[0]][-1]
plt.draw()
if name == 'res' and do_grid_resources == True:
grid_resources(cols)
return
nx = int(ceil(sqrt(len(gbks))))
ny = int(ceil(sqrt(len(gbks))))
f = plt.figure(1)
f.clear()
for i in range(len(gbks)):
xv,yv = divmod(i,nx)
ax = f.add_subplot('{0}{1}{2}'.format(nx,ny, i), xlim = [-.2,1.2], ylim = [-.2,1.2], frameon=True)
maptRNAs(gbks[i], ax)
tcols = {}
tct = mycolors.getct(64)
lvls = 7
functype = 'blank'
def maptRNAs(gbkfile, ax = None):
grec = SeqIO.parse(gbkfile, 'genbank')
grec = list(grec)[0].features
blank_speedfun = lambda x :\
x.type == 'tRNA' and 2 \
or x.type == 'gene' and 2 \
or x.type == 'CDS' and 2 \
or 0
speedfun = lambda x :\