def draw_minor_transition(ax, sc, d, a, b):
# transition from i to b
from numpy import logical_and
for i in range(4):
if i == b:
continue
d_ = d[d['Mn_seq_x'] == i]
if len(d_) == 0: continue
y_ = [
linspace(p_.maf_x, p_.maf_y, seq_size)
for p_ in d_[['maf_x', 'maf_y']].itertuples()
]
x_ = array(y_)
for j in range(len(d_)):
x_[j].fill(d_[duma_position].values[j])
c = [xlin for _ in range(len(x_))]
sc[a]['minor'].append(
ax.scatter(x_,
y_,
c=c,
cmap=mcols.cmap(dcolor[i][b]),
s=markersize))
# draw major scatter
y_ = get_uppery(y_)
x_ = [i[0] for i in x_]
sc[a]['major'].append(
ax.scatter(x_,
y_,
color=colors[a],
label=basepair[a],
s=markersize - 1))
def lambda_style(x): from mcolors import mcols if len(x['ct']) == 1: return self.colors[self.basepair.index(x['ct'].upper())] else: return mcols.cmap(self.dcolor[self.basepair.index(x['ct'][0].upper())][self.basepair.index(x['ct'][1].upper())])
def visualize(self):
import matplotlib.patches as mpatches
self.fig, self.ax = plt.subplots(3, 1, sharex=True)
self.ax[0].set_title('Click on legend rectangle to toggle data on/off', fontdict={'fontsize' : 8 })
self.fig.set_size_inches(12, 7, forward=True)
plt.subplots_adjust(left=0.05, bottom=0.15, right=0.98, hspace=0.15)
# bpdiff_trans = [] # major transition
self.ax = self.ax[::-1]
# major가 같은 것 들만
print('Run matplotlib...')
for i in range(len(self.bpdiff)):
sc = [ {'major' : [], 'minor': [] }, {'major' : [], 'minor': [] },
{'major' : [], 'minor': [] }, {'major' : [], 'minor': [] } ]
self.draw_vspans(self.ax[i], self.B.range_dumas)
for a in range(4):
cond1 = self.bpdiff[i]['Mj_seq_x'] == a
# major a -> minor b
for b in range(4):
if a == b:
# sc[a]['major'].append(None)
# sc[a]['minor'].append(None)
continue
# 1. minor가 같은 것들 처리 : 같은 색상
cond2 = self.bpdiff[i]['Mn_seq_y'] == b
# x는
cond3 = logical_or(self.bpdiff[i]['minor_x'] == 0, self.bpdiff[i]['Mn_seq_x'] == b)
cond3 = logical_and(cond2, cond3)
d = self.B.get_bpdiff_cond(index=i, cond=logical_and(cond1, cond3)) #bpdiff[i][ logical_and(cond1, cond3).values ]
if len(d) > 0:
y_ = [ linspace(d_.maf_x, d_.maf_y, self.seq_size) for d_ in d[['maf_x', 'maf_y']].itertuples() ]
x_ = array(y_)
for j in range(len(d)):
x_[j].fill( d[self.duma_position].values[j] )
c = [ self.xlin for _ in range(len(x_))]
sc[a]['minor'].append(self.ax[i].scatter(x_, y_, c=c, cmap=mcols.cmap(self.mcolor[b]), s=self.markersize, linewidth=0.0))
# draw major scatter
y_ = self.get_uppery(y_)
x_ = [ ii[0] for ii in x_]
sc[a]['major'].append(self.ax[i].scatter(x_, y_, color=self.basecolors[a], label=self.basepair[a], s=self.markersize-1))
# # 2. minor가 바뀌는 것들 처리 : colors diverging
# 각 basetype -> b type, target이 b, 즉, b로 변한것
cond2 = logical_and(self.bpdiff[i]['Mn_seq_x'] != b, self.bpdiff[i]['minor_x'] > 0)
cond3 = logical_and(cond2, self.bpdiff[i]['Mn_seq_y'] == b)
d = self.bpdiff[i][ logical_and(cond1, cond3).values ]
if len(d) > 0:
self.draw_minor_transition(self.ax[i], sc, d, a, b)
# end for b
#end for a
self.sct.append(sc)
self.ax[i].set_ylim([0, 50])
self.ax[i].set_ylabel('Variation of MAF(%)')
self.ax[i].set_title(self.ylabel[i], loc='left', fontdict={'fontsize':13, 'verticalalignment':'top', 'color':'black', 'backgroundcolor':'#FEFEFE'})
# ZoomSlider of Dumas position
zaxes = plt.axes([0.08, 0.07, 0.90, 0.03], facecolor='lightgoldenrodyellow')
self.zslider = ZoomSlider(zaxes, 'Dumas Position', valmin=self.B.minpos, valmax=self.B.maxpos, valleft=self.B.minpos, valright=self.B.maxpos, color='lightblue', valstep=1.0)
self.zslider.on_changed(self.update_xlim)
from legend import Legend
spatches = [ mpatches.Patch(color=self.basecolors[idx], label=self.basepair[idx]) for idx in range(4) ]
leg_basepair = Legend(self.fig, { 'spatches' : spatches, 'label' : self.basepair, 'bbox':(0.66, .91, 0.33, .102), 'loc' : 3,
'ncol' : 4, 'mode' : 'expand', 'borderaxespad' : 0.})
dumalabels = [ key for key in self.dumas.keys()]
spatches = [ mpatches.Patch(color='grey', label=dumalabels[idx]) for idx in range(3) ]
leg_dumas = Legend(self.fig, { 'spatches' : spatches, 'label' : dumalabels, 'bbox':(0.05, .91, 0.33, .102), 'loc' : 3,
'ncol' : 3, 'mode' : 'expand', 'borderaxespad' : 0.})
spatches = [ mpatches.Patch(color=['black', 'magenta'][idx], label=['base', 'variation'][idx]) for idx in range(2) ]
self.leg_filter = Legend(self.fig, { 'spatches' : spatches, 'label' : ['base_0.0', 'variation_5.0'], 'bbox':(0.40, .91, 0.24, .102), 'loc' : 3,
'ncol' : 3, 'mode' : 'expand', 'borderaxespad' : 0.})
for x in self.ax:
self.annot.append(x.annotate("", xy=(0,0), xytext=(20,-30),textcoords="offset points",
bbox=dict(boxstyle="round", fc="w"), arrowprops=dict(arrowstyle="->")))
# annotate over other axes
x.figure.texts.append(x.texts.pop())
#
# x.callbacks.connect('xlim_changed', xlim_changed_event)
for c in self.B.range_dumas.keys():
self.annot_gere[c] = []
ay_ = 0.85 if c == self.duma_Repeat else 0.7
if c == self.duma_ORF: ay_ = 1.
for d in self.dumas[c]:
self.annot_gere[c].append(self.ax[-1].annotate(d, xy=(self.B.range_dumas[c][d]['min'], 50*ay_), xytext=(-20,10),
textcoords="offset points", bbox=dict(boxstyle="round", fc="w"), arrowprops=dict(arrowstyle="fancy")))
for an_ in self.annot:
an_.set_visible(False)
an_.set_zorder(10)
for c in self.B.range_dumas.keys():
for an_ in self.annot_gere[c]:
an_.set_visible(False)
# legend pick event
self.fig.canvas.mpl_connect('pick_event', self.onpick)
leg_dumas.pick()
self.fig.canvas.mpl_connect("button_press_event", self.click_)
# ax[-1].text(105500, 49, 'IRS', fontdict={'fontsize':5})
# buttonaxes = plt.axes([0.89, .95, 0.1, 0.025])
# bnext = Button(buttonaxes, 'Export')
# bnext.on_clicked(ExportToParallelCoordGraph)
plt.show()
continue # 1. minor가 같은 것들 처리 : 같은 색상 cond2 = bpdiff[i]['Mn_seq_y'] == b # x는 cond3 = logical_or(bpdiff[i]['minor_x'] == 0, bpdiff[i]['Mn_seq_x'] == b) cond3 = logical_and(cond2, cond3) d = B.get_bpdiff_cond(index=i, cond=logical_and(cond1, cond3)) #bpdiff[i][ logical_and(cond1, cond3).values ] if len(d) > 0: y_ = [ linspace(d_.maf_x, d_.maf_y, seq_size) for d_ in d[['maf_x', 'maf_y']].itertuples() ] x_ = array(y_) for j in range(len(d)): x_[j].fill( d[duma_position].values[j] ) c = [ xlin for _ in range(len(x_))] sc[a]['minor'].append(ax[i].scatter(x_, y_, c=c, cmap=mcols.cmap(mcolor[b]), s=markersize, linewidth=0.0)) # draw major scatter y_ = get_uppery(y_) x_ = [ ii[0] for ii in x_] sc[a]['major'].append(ax[i].scatter(x_, y_, color=colors[a], label=basepair[a], s=markersize-1)) # # 2. minor가 바뀌는 것들 처리 : colors diverging # 각 basetype -> b type, target이 b, 즉, b로 변한것 cond2 = logical_and(bpdiff[i]['Mn_seq_x'] != b, bpdiff[i]['minor_x'] > 0) cond3 = logical_and(cond2, bpdiff[i]['Mn_seq_y'] == b) d = bpdiff[i][ logical_and(cond1, cond3).values ] if len(d) > 0: draw_minor_transition(ax[i], sc, d, a, b) # end for b #end for a
cond3 = logical_and(cond2, cond3)
d = bpdiff[i][logical_and(cond1, cond3).values]
if len(d) > 0:
y_ = [
linspace(d_.maf_x, d_.maf_y, seq_size)
for d_ in d[['maf_x', 'maf_y']].itertuples()
]
x_ = array(y_)
for j in range(len(d)):
x_[j].fill(d[duma_position].values[j])
c = [xlin for _ in range(len(x_))]
sc[a]['minor'].append(ax[i].scatter(x_,
y_,
c=c,
cmap=mcols.cmap(
mcolor[b]),
s=markersize,
linewidth=0.0))
# draw major scatter
y_ = get_uppery(y_)
x_ = [ii[0] for ii in x_]
sc[a]['major'].append(ax[i].scatter(x_,
y_,
color=colors[a],
label=basepair[a],
s=markersize - 1))
# # 2. minor가 바뀌는 것들 처리 : colors diverging
# 각 basetype -> b type, target이 b, 즉, b로 변한것
cond2 = logical_and(bpdiff[i]['Mn_seq_x'] != b,