def gate_cache(data):
ax = services.get_ax()
all_markers = None
if datatable:
all_markers = datatable.dims
data.text = ax.figure.text(0.01, 0.01, '', picker=1, size='x-small')
data.gater = Gater(ax, all_markers, rect, data.text)
def gate(x_marker, y_marker, rect, color_marker=None, datatable=None):
ax = services.get_ax()
def gate_cache(data):
ax = services.get_ax()
all_markers = None
if datatable:
all_markers = datatable.dims
data.text = ax.figure.text(0.01, 0.01, '', picker=1, size='x-small')
data.gater = Gater(ax, all_markers, rect, data.text)
data = services.cache((ax), gate_cache, True, False)
ax.set_xlabel(x_marker)
ax.set_ylabel(y_marker)
if color_marker:
data.text.set_text('Color: %s' % str(color_marker))
data.gater.renew_rect(rect)
if not rect:
rect = [None, None, None, None]
dim_ranges = [
DimRange(x_marker, rect[0], rect[2]),
DimRange(y_marker, rect[1], rect[3])
]
#if title:
# data.ax.set_title(title)
return (dim_ranges, x_marker, y_marker, rect, color_marker)
def gate_cache(data):
ax = services.get_ax()
all_markers = None
if datatable:
all_markers = datatable.dims
data.text = ax.figure.text(0.01, 0.01, '', picker=1, size='x-small')
data.gater = Gater(ax, all_markers, rect, data.text)
def gate(x_marker, y_marker, rect, color_marker=None, datatable=None):
ax = services.get_ax()
def gate_cache(data):
ax = services.get_ax()
all_markers = None
if datatable:
all_markers = datatable.dims
data.text = ax.figure.text(0.01, 0.01, '', picker=1, size='x-small')
data.gater = Gater(ax, all_markers, rect, data.text)
data = services.cache((ax), gate_cache, True, False)
ax.set_xlabel(x_marker)
ax.set_ylabel(y_marker)
if color_marker:
data.text.set_text('Color: %s' % str(color_marker))
data.gater.renew_rect(rect)
if not rect:
rect = [None, None, None, None]
dim_ranges = [
DimRange(x_marker, rect[0], rect[2]),
DimRange(y_marker, rect[1], rect[3])]
#if title:
# data.ax.set_title(title)
return (dim_ranges, x_marker, y_marker, rect, color_marker)
def kde2d(datatable,
markers,
range,
title=None,
norm_axis=None,
norm_axis_thresh=0.1,
*args,
**kargs):
ax = services.get_ax()
#markers = biology.markers.normalize_markers(markers)
def cached(data):
from mlabwrap import mlab
a, w = datatable.get_cols(markers[0], markers[1])
if range:
min_a = range[0]
max_a = range[2]
min_w = range[1]
max_w = range[3]
else:
min_w = min(w)
max_w = max(w)
min_a = min(a)
max_a = max(a)
points = datatable.get_points(markers[0], markers[1])
bandwidth, data.density, data.X, data.Y = mlab.kde2d(points,
256,
[[min_a, min_w]],
[[max_a, max_w]],
nout=4)
data = services.cache((datatable, markers, range, args, kargs), cached,
True, False)
display_data = data.density
if norm_axis == 'x':
max_dens_x = np.array([np.max(data.density, axis=1)]).T
if norm_axis_thresh:
max_dens_x[max_dens_x < norm_axis_thresh] = np.inf
data.density_x = data.density / max_dens_x
display_data = data.density_x
elif norm_axis == 'y':
max_dens_y = np.array([np.max(data.density, axis=0)])
if norm_axis_thresh:
max_dens_y[max_dens_y < norm_axis_thresh] = np.inf
data.density_y = data.density / max_dens_y
display_data = data.density_y
if title:
data.ax.set_title(title)
ax.set_xlabel(str(markers[0]) + ' ')
ax.set_ylabel(str(markers[1]) + ' ')
display_image(
display_data,
origin='lower',
extent=[data.X[0, 0], data.X[0, -1], data.Y[0, 0], data.Y[-1, 0]],
interpolation=None,
*args,
**kargs)
ax.figure.canvas.draw()
def color_table(datatable, dim_x=None, dim_y=None):
def cache(data):
ax = services.get_ax()
Picker(ax, datatable.dims)
ax = services.get_ax()
services.cache(ax, cache, True, False)
#print dim_x
#print dim_y
display_matrix(datatable.data, cmap=cm.jet)
ax.set_xticks(np.arange(len(datatable.dims)))
ax.set_yticks(np.arange(-1, len(datatable.dims)+1))
ax.set_xticklabels(datatable.dims)
ax.set_yticklabels([''] + datatable.dims)
ylabels = ax.yaxis.get_ticklabels()
xlabels = ax.xaxis.get_ticklabels()
for i in xrange(len(ylabels)):
x_index = i-1
ylabels[i].set_fontsize('xx-small')
if ylabels[i].get_text() == dim_y:
ylabels[i].set_weight('bold')
else:
ylabels[i].set_weight('normal')
if x_index >=0 and x_index < len(xlabels):
xlabels[x_index].set_fontsize('xx-small')
if ylabels[i].get_text() == dim_x :
xlabels[x_index].set_weight('bold')
else:
xlabels[x_index].set_weight('normal')
xlabels[x_index].set_rotation(90)
#ax.update_params(left=0, bottom=0)
ax.figure.canvas.draw()
return (dim_x, dim_y)
def create_data(data):
data.ax = services.get_ax()
data.line, = data.ax.plot([0], [0])
data.predefined_axes = False
if not None in (x_min, x_max, y_min, y_max):
data.predefined_axes = True
data.ax.set_xlim(x_min, x_max)
data.ax.set_ylim(y_min, y_max)
def create_data(data):
data.ax = services.get_ax()
data.line, = data.ax.plot([0], [0])
data.predefined_axes = False
if not None in (x_min, x_max, y_min, y_max):
data.predefined_axes = True
data.ax.set_xlim(x_min, x_max)
data.ax.set_ylim(y_min, y_max)
def create_data(data):
#logging.info('yoooo')
data.ax = services.get_ax()
#from matplotlib.colors import LightSource
#ls = LightSource(azdeg=0,altdeg=65)
#rgb = ls.shade(Z, cm.jet)
data.image = data.ax.imshow(Z, extent=extent, *args, **kargs)
data.colorbar = data.ax.figure.colorbar(data.image)
data.ax.set_aspect('auto')
def create_data(data):
#logging.info('yoooo')
data.ax = services.get_ax()
#from matplotlib.colors import LightSource
#ls = LightSource(azdeg=0,altdeg=65)
#rgb = ls.shade(Z, cm.jet)
data.image = data.ax.imshow(Z, extent=extent, *args, **kargs)
data.colorbar = data.ax.figure.colorbar(data.image)
data.ax.set_aspect('auto')
def kde2d(datatable, markers, range, title=None, norm_axis=None, norm_axis_thresh = 0.1, *args, **kargs):
ax = services.get_ax()
#markers = biology.markers.normalize_markers(markers)
def cached(data):
from mlabwrap import mlab
a, w = datatable.get_cols(markers[0], markers[1])
if range:
min_a = range[0]
max_a = range[2]
min_w = range[1]
max_w = range[3]
else:
min_w = min(w)
max_w = max(w)
min_a = min(a)
max_a = max(a)
points = datatable.get_points(markers[0], markers[1])
bandwidth,data.density, data.X, data.Y = mlab.kde2d(
points, 256,
[[min_a, min_w]],
[[max_a, max_w]],
nout=4)
data = services.cache((datatable, markers, range, args, kargs), cached, True, False)
display_data = data.density
if norm_axis == 'x':
max_dens_x = np.array([np.max(data.density, axis=1)]).T
if norm_axis_thresh:
max_dens_x[max_dens_x < norm_axis_thresh] = np.inf
data.density_x = data.density / max_dens_x
display_data = data.density_x
elif norm_axis == 'y':
max_dens_y = np.array([np.max(data.density, axis=0)])
if norm_axis_thresh:
max_dens_y[max_dens_y < norm_axis_thresh] = np.inf
data.density_y = data.density / max_dens_y
display_data = data.density_y
if title:
data.ax.set_title(title)
ax.set_xlabel(str(markers[0]) + ' ')
ax.set_ylabel(str(markers[1]) + ' ')
display_image(
display_data,
origin='lower',
extent=[
data.X[0,0],
data.X[0,-1],
data.Y[0,0],
data.Y[-1,0]],
interpolation=None, *args, **kargs)
ax.figure.canvas.draw()
def dim_choose(x_marker, y_marker, datatable=None):
ax = services.get_ax()
def gate_cache(data):
ax = services.get_ax()
all_markers = None
if datatable:
all_markers = datatable.dims
data.gater = Gater(ax, all_markers, None, None, False, True)
data = services.cache((ax), gate_cache, True, False)
ax.set_ylabel(y_marker)
ax.set_xlabel(x_marker)
return (x_marker, y_marker)
def dim_color_choose(x_marker, y_marker, color_marker, datatable=None):
ax = services.get_ax()
def gate_cache(data):
ax = services.get_ax()
all_markers = None
if datatable:
all_markers = datatable.dims
data.text = ax.figure.text(0.01, 0.01, '', picker=1, size='x-small')
data.gater = Gater(ax, all_markers, None, data.text, False, True)
data = services.cache((ax), gate_cache, True, False)
ax.set_ylabel(y_marker)
ax.set_xlabel(x_marker)
data.text.set_text('Color: %s' % str(color_marker))
return (x_marker, y_marker, color_marker)
def dim_choose(x_marker, y_marker, datatable=None):
ax = services.get_ax()
def gate_cache(data):
ax = services.get_ax()
all_markers = None
if datatable:
all_markers = datatable.dims
data.gater = Gater(ax, all_markers, None, None, False, True)
data = services.cache((ax), gate_cache, True, False)
ax.set_ylabel(y_marker)
ax.set_xlabel(x_marker)
return (x_marker, y_marker)
def dim_color_choose(x_marker, y_marker, color_marker, datatable=None):
ax = services.get_ax()
def gate_cache(data):
ax = services.get_ax()
all_markers = None
if datatable:
all_markers = datatable.dims
data.text = ax.figure.text(0.01, 0.01, '', picker=1, size='x-small')
data.gater = Gater(ax, all_markers, None, data.text, False, True)
data = services.cache((ax), gate_cache, True, False)
ax.set_ylabel(y_marker)
ax.set_xlabel(x_marker)
data.text.set_text('Color: %s' % str(color_marker))
return (x_marker, y_marker, color_marker)
def gatex(x_marker, y_text, rect, datatable=None):
ax = services.get_ax()
def gate_cache(data):
ax = services.get_ax()
all_markers = None
if datatable:
all_markers = datatable.dims
data.gater = Gater(ax, all_markers, rect, None, True)
data = services.cache((ax), gate_cache, True, False)
ax.set_xlabel(x_marker)
ax.set_ylabel(y_text)
data.gater.renew_rect(rect)
if not rect:
rect = [None, None]
dim_ranges = [DimRange(x_marker, rect[0], rect[1])]
return (dim_ranges, x_marker, rect)
def gatex(x_marker, y_text, rect, datatable=None):
ax = services.get_ax()
def gate_cache(data):
ax = services.get_ax()
all_markers = None
if datatable:
all_markers = datatable.dims
data.gater = Gater(ax, all_markers, rect, None, True)
data = services.cache((ax), gate_cache, True, False)
ax.set_xlabel(x_marker)
ax.set_ylabel(y_text)
data.gater.renew_rect(rect)
if not rect:
rect = [None, None]
dim_ranges = [DimRange(x_marker, rect[0], rect[1])]
return (dim_ranges, x_marker, rect)
def color_table(datatable, dim_x=None, dim_y=None):
def cache(data):
ax = services.get_ax()
Picker(ax, datatable.dims)
ax = services.get_ax()
services.cache(ax, cache, True, False)
#print dim_x
#print dim_y
display_matrix(datatable.data, cmap=cm.jet)
ax.set_xticks(np.arange(len(datatable.dims)))
ax.set_yticks(np.arange(-1, len(datatable.dims) + 1))
ax.set_xticklabels(datatable.dims)
ax.set_yticklabels([''] + datatable.dims)
ylabels = ax.yaxis.get_ticklabels()
xlabels = ax.xaxis.get_ticklabels()
for i in xrange(len(ylabels)):
x_index = i - 1
ylabels[i].set_fontsize('xx-small')
if ylabels[i].get_text() == dim_y:
ylabels[i].set_weight('bold')
else:
ylabels[i].set_weight('normal')
if x_index >= 0 and x_index < len(xlabels):
xlabels[x_index].set_fontsize('xx-small')
if ylabels[i].get_text() == dim_x:
xlabels[x_index].set_weight('bold')
else:
xlabels[x_index].set_weight('normal')
xlabels[x_index].set_rotation(90)
#ax.update_params(left=0, bottom=0)
ax.figure.canvas.draw()
return (dim_x, dim_y)
def cache(data):
ax = services.get_ax()
Picker(ax, datatable.dims)
def gate_cache(data):
ax = services.get_ax()
all_markers = None
if datatable:
all_markers = datatable.dims
data.gater = Gater(ax, all_markers, rect, None, True)
def gate_cache(data):
ax = services.get_ax()
all_markers = None
if datatable:
all_markers = datatable.dims
data.gater = Gater(ax, all_markers, rect, None, True)
def create_data(data):
data.ax = services.get_ax()
data.image = data.ax.matshow(Z, *args, **kargs)
def create_data(data): data.ax = services.get_ax() data.image = data.ax.matshow(Z, *args, **kargs)
def cache(data): ax = services.get_ax() Picker(ax, datatable.dims)
def fix_axis():
ax = services.get_ax()
def fix_axis(): ax = services.get_ax()