def draw_points_lines_crs(points: torch.Tensor,
lines: torch.Tensor,
crs: torch.Tensor,
filename,
size=1,
lw=1,
clw=1,
pcols=None,
lcols=None,
crscols=None,
canvas_clip=None,
svg=False):
if canvas_clip is not None:
c = canvas.canvas([canvas.clip(path.rect(*canvas_clip))])
else:
c = canvas.canvas()
draw_points_to_canvas(c, points, size, pcols)
draw_lines_to_canvas(c, lines, lw, lcols)
draw_crs_to_canvas(c, crs, clw, crscols)
if svg:
c.writeSVGfile(file=filename)
else:
c.writePDFfile(file=filename)
def draw(self, r=5):
c = canvas.canvas()
x_centre = r + 1
y_centre = r + 1
angle_diff = 2*math.pi/self.n
def get_pos(index):
x_pos = x_centre + math.sin(index*angle_diff)*r
y_pos = y_centre + math.cos(index*angle_diff)*r
return x_pos, y_pos
# nodes
for i in range(self.n):
x, y = get_pos(i)
c.stroke(path.circle(x, y, 1))
c.text(x, y, i)
# edges
for i in range(self.n):
for j in range(self.n):
if math.isnan(self.adj_mat[i, j]):
continue
x1, y1 = get_pos(i)
x2, y2 = get_pos(j)
x_offset = (x2 - x1)/math.sqrt((x1 - x2)**2 + (y1 - y2)**2)
y_offset = (y2 - y1)/math.sqrt((x1 - x2)**2 + (y1 - y2)**2)
arc = path.line(x1 + x_offset, y1 + y_offset, x2 - x_offset, y2 - y_offset)
c.stroke(arc, [deco.earrow()])
c.text((x1 + x2)/2 + x_offset, (y1 + y2)/2 + y_offset, self.adj_mat[i, j]) # moved towards the end pt
c.writePDFfile("graph")
def main():
A4_lsc = document.paperformat(
document.paperformat.A4.height, document.paperformat.A4.width)
text.set(text.UnicodeEngine, fontname="cmss12", size=12)
pages = []
for i in (
('C', 'Am', 'C#', 'A#m'),
('D', 'Bm', 'D#', 'Cm'),
('E', 'C#m', 'F', 'Dm'),
('F#', 'D#m', 'G', 'Em'),
('G#', 'Fm', 'A', 'F#m'),
('A#', 'Gm', 'B', 'G#m')
):
c = canvas.canvas()
c.text(0, 32, f'{i[0]} Pentatonic Scale')
Pentatonic(0, 26, i[0]).render(c, intervals=True)
c.text(0, 24, f'{i[1]} Pentatonic Scale')
Pentatonic(0, 18, i[1]).render(c, intervals=True)
c.text(0, 16, f'{i[2]} Pentatonic Scale')
Pentatonic(0, 10, i[2]).render(c, intervals=True)
c.text(0, 8, f'{i[3]} Pentatonic Scale')
Pentatonic(0, 2, i[3]).render(c, intervals=True)
page = document.page(c, paperformat=A4_lsc, fittosize=1, margin=2)
pages.append(page)
doc = document.document(pages=pages)
doc.writePDFfile("pentatonic")
def array34(arange, hlshape=None):
c = canvas.canvas()
if hlshape is None:
c.text(2, 3.3, 'shape=(3, 4)', [text.halign.center])
else:
c.text(2, 3.3, 'shape=%s' % repr(hlshape), [text.halign.center])
if hlshape is not None:
if len(hlshape) == 1:
hlshape = (1, hlshape[0])
if arange:
gridcolor = color.grey(0)
else:
gridcolor = color.grey(0.5)
if hlshape is None:
arange = True
elif (hlshape[0] in (1, 3)) and (hlshape[1] in (1, 4)):
arange = False
else:
arange = None
drawgrid(c, 4, 3, 0, gridcolor, arange=arange)
if hlshape is not None:
c.stroke(path.rect(0, 3, hlshape[1], -hlshape[0]),
[deco.filled([color.rgb(1, 0.8, 0.4)])])
drawgrid(c, hlshape[1], hlshape[0], 3 - hlshape[0], arange=False)
if arange is None:
alertcolor = color.rgb(0.6, 0, 0)
c.stroke(path.line(0, 0, 4, 3), [alertcolor, style.linewidth.Thick])
c.stroke(path.line(0, 3, 4, 0), [alertcolor, style.linewidth.Thick])
return c
def paintcolumn(self, plotitems):
"creates the layout of a key column"
c = canvas.canvas()
self.dist_pt = unit.topt(self.dist)
self.hdist_pt = unit.topt(self.hdist)
self.vdist_pt = unit.topt(self.vdist)
self.symbolwidth_pt = unit.topt(self.symbolwidth)
self.symbolheight_pt = unit.topt(self.symbolheight)
self.symbolspace_pt = unit.topt(self.symbolspace)
titleboxes = []
for plotitem in plotitems:
titlebox = c.texrunner.text_pt(
0, 0, plotitem.title, self.defaulttextattrs + self.textattrs)
titlebox.plotitem = plotitem
titleboxes.append(titlebox)
dy_pt = box.tile_pt(titleboxes, self.dist_pt, 0, -1)
box.linealignequal_pt(titleboxes,
self.symbolwidth_pt + self.symbolspace_pt, 1, 0)
y_pt = -0.5 * self.symbolheight_pt + titleboxes[0].center[1]
for titlebox in titleboxes:
titlebox.plotitem.key_pt(c, 0, y_pt, self.symbolwidth_pt,
self.symbolheight_pt)
y_pt -= dy_pt
for titlebox in titleboxes:
c.insert(titlebox)
return c
def plot_dataset_ranges(data0, data1, width, height):
binsizes = numpy.unique(data0['binsize'])
ho = 1.1
ho2 = 0.2
vo = 1.0
plot_width = (width - ho - ho2 * 3) / 4.0
plot_height = height - vo
c = canvas.canvas()
for i, binsize in enumerate(binsizes):
if i == 0:
ylabel = True
else:
ylabel = False
img = plot_single_range(data0, data1, binsize, plot_width, plot_height,
ylabel)
c.insert(img, [trafo.translate(ho + i * (plot_width + ho2), vo - 0.3)])
c.text(
0, plot_height * 0.5 + vo - 0.3, r"$r_{Poisson} - r_{binomial}$",
[text.halign.center, text.valign.top,
text.size(-2),
trafo.rotate(90)])
c.text(plot_width * 2 + ho + 1.5 * ho2, 0, "Interaction Range (bp)",
[text.halign.center, text.valign.bottom,
text.size(-3)])
c.text(0, height, 'a', [text.halign.left, text.valign.top, text.size(-1)])
return c
def plot_dataset_ranges(data0, data1, width):
methods = data0.keys()
binsizes = numpy.unique(data0[methods[0]]['binsize'])
ho = 0.8
ho2 = 0.25
vo = 0.7
vo2 = 0.4
spacer = 0.0
plot_width = (2 * width - ho * 2 - ho2 - spacer) / 2
plot_height = width - vo - vo2
c = canvas.canvas()
for i, binsize in enumerate(binsizes):
img = plot_single_range(data0, data1, binsize, plot_width, plot_width,
vo, vo2)
c.insert(img, [
trafo.translate(
(plot_width + spacer + ho) * (i % 2) + ho2 + ho,
(1 - i / 2) * (plot_height + spacer + vo + vo2) + vo)
])
c.text(
0, plot_height + 0.5 * spacer + vo + vo2, r"$r_{0K} - r_{500K}$",
[text.halign.center, text.valign.top,
text.size(-2),
trafo.rotate(90)])
c.text(plot_width + ho2 + spacer * 0.5 + ho, 0, "Interaction Range (bp)",
[text.halign.center, text.valign.bottom,
text.size(-3)])
c.text(0, width * 2 + spacer, 'a',
[text.halign.left, text.valign.top,
text.size(-1)])
return c
def try_size(self, frame_shape, file=''):
# first we setup the block anew
self.frame = Frame(self.dimensions, self.num_vectors, self.steps)
first_frame_shape = self.get_first_frame_shape()
self.frame.seed_frame(first_frame_shape)
cross_vectors = self.get_cross_vectors()
for vector in cross_vectors:
self.frame.populate(vector)
# now we try to grow our block to the right size
if not self.frame.grow_to_size(frame_shape):
return None
print '--> generating linear system'
linear_system = self.generate_linear_system()
print ' size is %s, %s' % (len(linear_system), len(linear_system[0]))
print '--> trying to find a solution'
vector_solution = self.solve(linear_system)
if vector_solution is None:
print '--> solution not found'
return None
else:
print '--> solution found'
solution = self.normalize_solution(vector_solution)
self.set_edge_weights(solution)
if file:
c = canvas.canvas()
self.draw_edges(c)
c.writePDFfile(file)
def plot_dataset_ranges(data, width, spacer):
methods = data.keys()
binsizes = numpy.unique(data[methods[0]]['binsize'])
plot_width = width - 0.4
plot_height = plot_width + 0.2
c = canvas.canvas()
for i, binsize in enumerate(binsizes):
img = plot_single_range(data, binsize, plot_width, plot_height)
c.insert(img, [
trafo.translate(
(plot_width + spacer) * i + 0.4, 0.4 + spacer * 0.5)
])
c.text(
0, plot_height * 0.5 + 0.2 + spacer * 0.75, "Dataset correlation",
[text.halign.center, text.valign.top,
text.size(-3),
trafo.rotate(90)])
c.text(plot_width * 2 + spacer * 1.5 + 0.4, 0.35, "Interaction range (bp)",
[text.halign.center, text.valign.bottom,
text.size(-3)])
c.fill(path.rect(0.4, 0.025, 0.2, 0.2), [color.rgb.black])
c.text(0.7, 0.125, "HiFive-Express using raw reads",
[text.halign.left, text.valign.middle,
text.size(-2)])
c.fill(path.rect(plot_width * 2 + spacer * 1.5, 0.025, 0.2, 0.2),
[color.rgb.red])
c.text(plot_width * 2 + spacer * 1.5 + 0.3, 0.125,
"HiFive-Express using distance-corrected reads",
[text.halign.left, text.valign.middle,
text.size(-2)])
return c, plot_height + 0.4 + spacer
def Draw(self, file):
# this simply creates a canvas, draws the interior and exterior and
# then exports it as a PDF
c = canvas.canvas()
DrawBlock(self.block, c)
DrawBlock(self.interior, c)
c.writePDFfile(file)
def make_stride_figure(lowerstride, upperstride=1, nrentries=6):
c = canvas.canvas()
ht = 0.5
wd = 2
dist = 0.2
textcolor = color.hsb(0.02, 1, 0.6)
for n in range(nrentries):
x = n*(wd+dist)
c.stroke(path.rect(x, 0, wd, ht))
c.text(x+0.5*wd, 0.5*ht, str(n), [text.halign.center, text.valign.middle])
for n in range(nrentries-1):
x = n*(wd+dist)
c.stroke(path.curve(x-dist/3, ht+0.5*dist,
x+0.3*wd, ht+3*dist,
x+0.7*wd, ht+3*dist,
x+wd+dist/3, ht+0.5*dist),
[deco.earrow.large])
c.text(x+0.5*wd, ht+3.2*dist, r'\Large 8', [text.halign.center, textcolor])
if lowerstride:
for n in range((nrentries-1)//lowerstride):
x = n*lowerstride*(wd+dist)
c.stroke(path.curve(x-dist/3, -0.5*dist,
x+0.5*wd, -5*dist,
x+(lowerstride-0.5)*wd+lowerstride*dist, -5*dist,
x+lowerstride*wd+(lowerstride-0.7)*dist, -0.5*dist),
[deco.earrow.large])
c.text(x+0.5*lowerstride*wd+dist,-5.2*dist, r'\Large %i' % (lowerstride*8),
[text.halign.center, text.valign.top, textcolor])
return c
def plot_dataset_ranges(data, width, label):
methods = data.keys()
binsizes = numpy.unique(data[methods[0]]['binsize'])
ho = 0.4
ho2 = 0.4
vo = 0.6
spacer = 0.25
plot_width = (width - ho * 2 -
(binsizes.shape[0] - 1) * spacer) / binsizes.shape[0] - ho2
plot_height = plot_width
c = canvas.canvas()
for i, binsize in enumerate(binsizes):
img = plot_single_range(data, binsize, plot_width, plot_width)
c.insert(img, [
trafo.translate((plot_width + spacer) * i + ho2 * (i + 1) + ho, vo)
])
c.text(
0, plot_height * 0.5 + vo, "Correlation",
[text.halign.center, text.valign.top,
text.size(-3),
trafo.rotate(90)])
c.text(width, plot_height * 0.5 + vo, label, [
text.halign.center, text.valign.top,
text.size(-3),
trafo.rotate(-90)
])
c.text((plot_width + ho2) * 2 + spacer * 1.5 + ho, 0,
"Interaction Range (bp)",
[text.halign.center, text.valign.bottom,
text.size(-3)])
return c, plot_height + vo + 0.3
def main():
out_fname = sys.argv[1]
basedir = '/'.join(os.path.dirname(os.path.realpath(__file__)).split('/')[:-2])
mm9_methods = {
'0 pseudo-counts':'%s/Analysis/hifive_mm9_ESC_bin_correlations.txt' % basedir,
'1 pseudo-count':'%s/Analysis/hifive_mm9_ESC_binPC1_correlations.txt' % basedir,
'3 pseudo-counts':'%s/Analysis/hifive_mm9_ESC_binPC3_correlations.txt' % basedir,
'6 pseudo-counts':'%s/Analysis/hifive_mm9_ESC_binPC6_correlations.txt' % basedir,
'HiCPipe':'%s/Analysis/hicpipe_mm9_ESC_correlations.txt' % basedir,
}
mm9_data = load_data(mm9_methods)
width = 16.8
spacer = 0.4
overall_width = (width - spacer * 2) / 2.6
c = canvas.canvas()
prob_ranges_img, prob_ranges_height = plot_dataset_ranges(mm9_data, width)
prob_ranges_img.text(0, prob_ranges_height, 'a',
[text.halign.left, text.valign.top, text.size(-1)])
c.insert(prob_ranges_img)
overall_height = prob_ranges_height * 0.6
hifive_overall_img = plot_overall(mm9_data, overall_width, overall_height, 'cis')
hifive_overall_img.text(0, overall_height + 0.1, 'b',
[text.halign.left, text.valign.top, text.size(-1)])
c.insert(hifive_overall_img, [trafo.translate(0, -overall_height - spacer)])
hifive_overall_img = plot_overall(mm9_data, overall_width, overall_height, 'trans')
hifive_overall_img.text(0, overall_height + 0.1, 'c',
[text.halign.left, text.valign.top, text.size(-1)])
c.insert(hifive_overall_img,
[trafo.translate(width - overall_width, -overall_height - spacer)])
c.insert(plot_key(overall_width * 0.6 + 0.4, overall_height, mm9_data),
[trafo.translate(overall_width + spacer + 0.6, -overall_height - spacer)])
c.writePDFfile(out_fname)
def main():
width = 16.8
out_fname = sys.argv[1]
basedir = "%s/Analysis/Timing" % '/'.join(os.path.dirname(os.path.realpath(__file__)).split('/')[:-2])
data_fnames = {
"HiFive-Probability":{'0':"%s/hifive_data" % basedir, '1':"%s/hifive_project" % basedir,
'3':'%s/hifive_prob' % basedir, '4':"%s/hifive_prob_heatmap" % basedir},
"HiFive-Binning":{'0':"%s/hifive_data" % basedir, '1':"%s/hifive_project_nodist" % basedir,
'3':'%s/hifive_bin' % basedir, '4':"%s/hifive_bin_heatmap" % basedir},
"HiFive-Express":{'0':"%s/hifive_data" % basedir, '1':"%s/hifive_project" % basedir,
'3':'%s/hifive_exp' % basedir, '4':"%s/hifive_exp_heatmap" % basedir},
"HiFive-ExpressKR":{'0':"%s/hifive_data" % basedir, '1':"%s/hifive_project_nodist" % basedir,
'3':'%s/hifive_expKR' % basedir, '4':"%s/hifive_expKR_heatmap" % basedir},
"HiFive-ExpressKR w/distance":{'0':"%s/hifive_data" % basedir, '1':"%s/hifive_project" % basedir,
'3':'%s/hifive_expKRdist' % basedir, '4':"%s/hifive_expKRdist_heatmap" % basedir},
"HiCPipe":{'0':"%s/bam2raw" % basedir, '1':"%s/hicpipe_data" % basedir,
'2':'%s/hicpipe_binning' % basedir, '3':'%s/hicpipe_norm' % basedir,
'4':'%s/hicpipe_heatmap' % basedir},
"HiCLib":{'0':"%s/hiclib_mapping" % basedir, '1':'%s/hiclib_data' % basedir,
'3':"%s/hiclib_norm" % basedir, '4':'%s/hiclib_heatmap' % basedir},
"HiCNorm":{'0':"%s/bam2raw" % basedir, '1':"%s/hicpipe_data" % basedir,
"2":"%s/hicnorm_data" % basedir, '3':'%s/hicnorm_norm' % basedir},
}
data = load_data(data_fnames)
c = canvas.canvas()
c.insert(plot_bargraph(data, width, 4.0), [trafo.translate(4.0, 0)])
c.insert(plot_key(width * 0.3, 1.5), [trafo.translate(width * 0.75 - 1.0, 0.2)])
c.writePDFfile(out_fname)
def find(self, file=''):
"""
This is the meat of the algorithm. It takes the frame and runs the steps outlined
in the report. So if you've read the report this should be pretty self explanatory.
"""
dimension = 0
while True:
print '--> generating linear system'
linear_system = self.generate_linear_system()
print ' size is %s, %s' % (len(linear_system), len(linear_system[0]))
print '--> trying to find a solution'
vector_solution = self.solve(linear_system)
if vector_solution is None:
print '--> solution not found'
print '--> doubling along dimension %s' % dimension
self.frame.double(dimension)
dimension = (dimension + 1) % self.dimensions
else:
break
solution = self.normalize_solution(vector_solution)
self.set_edge_weights(solution)
if file:
c = canvas.canvas()
self.draw_edges(c)
c.writePDFfile(file)
def main():
out_fname = sys.argv[1]
basedir = '/'.join(
os.path.dirname(os.path.realpath(__file__)).split('/')[:-2])
mm9_methods = {
'distance-corrected':
'%s/Analysis/hifive_mm9_ESC_exp_correlations.txt' % basedir,
'raw': '%s/Analysis/hifive_mm9_ESC_expdist_correlations.txt' % basedir,
}
mm9_data = load_data(mm9_methods)
width = 16.8
spacer = 0.4
plot_width = (width - spacer * 4) / 5
c = canvas.canvas()
mm9_ranges_img, mm9_ranges_height = plot_dataset_ranges(
mm9_data, plot_width, spacer)
mm9_ranges_img.text(0, mm9_ranges_height, 'b',
[text.halign.left, text.valign.top,
text.size(-1)])
c.insert(mm9_ranges_img, [trafo.translate(plot_width + spacer, 0)])
mm9_overall_img = plot_overall(mm9_data, plot_width - spacer,
(mm9_ranges_height - spacer) - 0.3)
c.text(0, mm9_ranges_height, 'a',
[text.halign.left, text.valign.top,
text.size(-1)])
c.insert(mm9_overall_img, [trafo.translate(0, 0.4)])
c.writePDFfile(out_fname)
def array34(arange, hlshape=None):
c = canvas.canvas()
if hlshape is None:
c.text(2, 3.3, 'shape=(3, 4)', [text.halign.center])
else:
c.text(2, 3.3, 'shape=%s' % repr(hlshape), [text.halign.center])
if hlshape is not None:
if len(hlshape) == 1:
hlshape = (1, hlshape[0])
if arange:
gridcolor = color.grey(0)
else:
gridcolor = color.grey(0.5)
if hlshape is None:
arange = True
elif (hlshape[0] in (1, 3)) and (hlshape[1] in (1, 4)):
arange = False
else:
arange = None
drawgrid(c, 4, 3, 0, gridcolor, arange=arange)
if hlshape is not None:
c.stroke(path.rect(0, 3, hlshape[1], -hlshape[0]),
[deco.filled([color.rgb(1, 0.8, 0.4)])])
drawgrid(c, hlshape[1], hlshape[0], 3-hlshape[0], arange=False)
if arange is None:
alertcolor = color.rgb(0.6, 0, 0)
c.stroke(path.line(0, 0, 4, 3), [alertcolor, style.linewidth.Thick])
c.stroke(path.line(0, 3, 4, 0), [alertcolor, style.linewidth.Thick])
return c
def guide_layer(holes):
guide_size = 1.2
# Get guide fiber information
iguide = np.nonzero(np.array(holes['holetype']) == b'GUIDE')[0]
guide_xfocal = np.array(holes['xfocal'])[iguide]
guide_yfocal = np.array(holes['yfocal'])[iguide]
guidenum = np.array(holes['iguide'])[iguide]
# Set up object to print
clippath = path.circle(0., 0., interior_radius)
clipobject = canvas.clip(clippath)
interior = canvas.canvas([clipobject])
for indx in range(len(guide_xfocal)):
interior.stroke(
path.rect((guide_yfocal[indx] / 10.) - guide_size * 0.5,
(guide_xfocal[indx] / 10.) - guide_size * 0.5,
guide_size, guide_size),
[style.linewidth.THick, color.cmyk.Black])
interior.text(
(guide_yfocal[indx] / 10.) + guide_size * 0.66,
(guide_xfocal[indx] / 10.),
r"\font\myfont=cmr10 at 35pt {\myfont " + str(guidenum[indx]) +
"}", [text.halign.boxleft, text.valign.middle, text.size.Huge])
return interior
def main():
out_fname = sys.argv[1]
basedir = '/'.join(os.path.dirname(os.path.realpath(__file__)).split('/')[:-2])
mm9_methods = {
'HiFive-Probability':'%s/Analysis/hifive_mm9_ESC_prob_correlations.txt' % basedir,
'HiFive-Express':'%s/Analysis/hifive_mm9_ESC_exp_correlations.txt' % basedir,
'HiFive-Binning':'%s/Analysis/hifive_mm9_ESC_bin_correlations.txt' % basedir,
}
dist_methods = {
'HiFive-Probability':'%s/Analysis/hifive_mm9_ESC_probnodist_correlations.txt' % basedir,
'HiFive-Express':'%s/Analysis/hifive_mm9_ESC_expnodist_correlations.txt' % basedir,
'HiFive-Binning':'%s/Analysis/hifive_mm9_ESC_binnodist_correlations.txt' % basedir,
}
mm9_data = load_data(mm9_methods)
dist_data = load_data(dist_methods)
width = 16.8
spacer = 0.4
range_width = (width - spacer) / 3.0
c = canvas.canvas()
mm9_ranges_img = plot_dataset_ranges(mm9_data, dist_data, range_width)
c.insert(mm9_ranges_img)
mm9_overall_img = plot_overall(mm9_data, dist_data, range_width, range_width)
mm9_overall_img.text(0, range_width, 'b',
[text.halign.left, text.valign.top, text.size(-1)])
c.insert(mm9_overall_img, [trafo.translate(range_width * 2 + spacer, range_width)])
c.insert(plot_key(range_width / 2, range_width / 2),
[trafo.translate(range_width * 2.25 + spacer, range_width * 0.25)])
c.writePDFfile(out_fname)
def make_picture_for_two_vertices():
c = canvas.canvas()
c.stroke(path.rect(0, 0, 12, 1))
c.stroke(path.rect(1, 0, 1, 1), [style.linewidth.THICK])
c.stroke(path.rect(5, 0, 1, 1), [style.linewidth.THICK])
c.stroke(path.rect(7, 0, 1, 1), [style.linewidth.THICK])
c.stroke(path.rect(10, 0, 1, 1), [style.linewidth.THICK])
c.stroke(path.line(-0.5, 0.5, -0.5, 6), [deco.earrow(size=0.2)])
c.stroke(path.line(1.5, 0.5, 1.5, 5), [deco.earrow(size=0.2)])
c.stroke(path.line(5.5, 0.5, 5.5, 4), [deco.earrow(size=0.2)])
c.stroke(path.line(7.5, 0.5, 7.5, 3), [deco.earrow(size=0.2)])
c.stroke(path.line(10.5, 0.5, 10.5, 2), [deco.earrow(size=0.2)])
c.stroke(path.line(12.5, 0.5, 12.5, 1), [deco.earrow(size=0.2)])
c.stroke(path.line(5.5, 4, 8, 4), [style.linewidth.THIN])
c.stroke(path.line(7, 3, 8, 3), [style.linewidth.THIN])
c.text(7.5, 3.5, r"$\delta_i = l_i - l_{i + 1}$", [text.halign.boxcenter, text.valign.middle])
c.stroke(path.line(6, 0, 6, -1), [style.linewidth.THIN])
c.stroke(path.line(7, 0, 7, -1), [style.linewidth.THIN])
c.text(6.5, -0.4, r"$d_i$", [text.halign.boxcenter, text.valign.middle])
c.text(-0.5, 3, r"$l_0 = 1.0$", [text.halign.boxleft])
c.text(5.5, 2.5, r"$l_i$", [text.halign.boxright])
c.text(7.5, 2, r"$l_{i+1}$", [text.halign.boxleft])
c.text(12.5, 1.1, r"$l_{E+1} = 0.0$", [text.halign.boxcenter])
c.writePDFfile("test_picture.pdf")
def processPS(self, file, writer, context, registry, bbox):
if writer.mesh_as_bitmap:
from pyx import bitmap, canvas
from PIL import Image
c = canvas.canvas()
c.insert(self)
i = Image.open(c.pipeGS("pngalpha", resolution=writer.mesh_as_bitmap_resolution))
i.load()
b = bitmap.bitmap_pt(self.bbox().llx_pt, self.bbox().lly_pt, i)
# we slightly shift the bitmap to re-center it, as the bitmap might contain some additional border
# unfortunately we need to construct another bitmap instance for that ...
b = bitmap.bitmap_pt(self.bbox().llx_pt + 0.5*(self.bbox().width_pt()-b.bbox().width_pt()),
self.bbox().lly_pt + 0.5*(self.bbox().height_pt()-b.bbox().height_pt()), i)
b.processPS(file, writer, context, registry, bbox)
else:
thisbbox = self.bbox()
bbox += thisbbox
file.write("""<< /ShadingType 4
/ColorSpace %s
/BitsPerCoordinate 24
/BitsPerComponent 8
/BitsPerFlag 8
/Decode [%f %f %f %f %s]
/DataSource currentfile /ASCIIHexDecode filter /FlateDecode filter
>> shfill\n""" % (self.elements[0].nodes[0].value.colorspacestring(),
thisbbox.llx_pt, thisbbox.urx_pt, thisbbox.lly_pt, thisbbox.ury_pt,
" ".join(["0 1" for value in self.elements[0].nodes[0].value.to8bitbytes()])))
file.write_bytes(binascii.b2a_hex(zlib.compress(self.data(thisbbox))))
file.write(">\n")
def signature(self, deg_max=6, padded=False, has_border=False):
""" For a visualization of glyphs, lay out in a 2D grid PNG file. """
self.scale()
sig = canvas.canvas([trafo.rotate(90), trafo.mirror(0)])
scale = 1.5
if padded or has_border:
sig_margin = 0.2
x = (deg_max + 1) * scale + (1.5 * sig_margin)
border_path = path.path(path.moveto(0, 0), path.lineto(0, x),
path.lineto(x, x), path.lineto(x, 0),
path.closepath())
if padded:
border_color = color.cmyk.White
if has_border:
border_color = color.cmyk.Gray
sig.stroke(border_path, [
border_color,
trafo.translate(-sig_margin * 2, -sig_margin * 2),
style.linewidth(.025)
])
for index in self.glist:
if len(index) > 2:
c = degree_glyph(index[0], index[1], index[2],
(self.mincount, self.maxcount))
else:
c = degree_glyph(index[0], index[1], 1,
(self.mincount, self.maxcount))
sig.insert(c,
[trafo.translate(index[0] * scale, (index[1]) * scale)
]) # text writing requires full latex
return sig
def see_frame(self, file):
for edge in self.frame.coordinate_vectors:
edge.weight = edge.pin
for edge in self.frame.cross_vectors:
edge.weight = edge.pin
c = canvas.canvas()
self.draw_edges(c)
c.writePDFfile(file)
def __init__(self, nsquares):
self.nsquares = nsquares
self.corners = deque([np.array([0, 0]), np.array([1, 0]),
np.array([1, 1]), np.array([0, 1])])
self.counter = 1
self.initialize_pyx()
self.c = canvas.canvas()
self.draw()
def plot_key(width, height):
c = canvas.canvas()
w = height / 7.0
for i, meth in enumerate(methods):
c.fill(path.rect(1.0, (6 - i) * w - 0.1, 0.2, 0.2), [method_colors[meth]])
c.text(1.3, (6 - i) * w, "%s" % meth_names[meth],
[text.halign.left, text.valign.middle, text.size(-3)])
return c
def paint(self, plotitems):
"creates the layout of the key"
columndist_pt = unit.topt(self.columndist)
c = canvas.canvas()
itemspercolumn = (len(plotitems) + self.columns - 1) // self.columns
x_pt = 0
while plotitems:
subc = self.paintcolumn(plotitems[:itemspercolumn])
c.insert(subc, [trafo.translate_pt(x_pt, 0)])
x_pt += unit.topt(subc.bbox().width()) + columndist_pt
del plotitems[:itemspercolumn]
if self.keyattrs is not None:
newc = canvas.canvas()
newc.draw(c.bbox().enlarged(self.border).path(), self.keyattrs)
newc.insert(c)
c = newc
return c
def paint(self, plotitems):
"creates the layout of the key"
columndist_pt = unit.topt(self.columndist)
c = canvas.canvas()
itemspercolumn = (len(plotitems) + self.columns - 1) // self.columns
x_pt = 0
while plotitems:
subc = self.paintcolumn(plotitems[:itemspercolumn])
c.insert(subc, [trafo.translate_pt(x_pt, 0)])
x_pt += unit.topt(subc.bbox().width()) + columndist_pt
del plotitems[:itemspercolumn]
if self.keyattrs is not None:
newc = canvas.canvas()
newc.draw(c.bbox().enlarged(self.border).path(), self.keyattrs)
newc.insert(c)
c = newc
return c
def plot_key(width, height):
c = canvas.canvas()
step = height / float(len(method_colors))
for i, meth in enumerate(['HiFive-Probability', 'HiFive-Express', 'HiFive-Binning']):
c.fill(path.rect(0.2, height - step * (i + 0.5) - 0.1, 0.2, 0.2),
[method_colors[meth]])
c.text(0.5, height - step * (i + 0.5), meth, [text.halign.left, text.valign.middle, text.size(-2)])
return c
def backup():
inFolder = Path(args.input)
memTar = BytesIO()
tar = tarfile.open(fileobj=memTar, mode="x")
for itm in inFolder.iterdir():
tar.add(itm.resolve(), arcname=itm.relative_to(inFolder))
tar.close()
content = memTar.getvalue()
memTar.close()
content = compress(content)
b85Content = b85encode(content).decode("UTF-8")
pdf = document()
pdfPage = None
counter = 0
while b85Content:
b85Content = str(counter) + ">" + b85Content
chunk, b85Content = maxSplit(b85Content)
if b85Content is None:
chunk = chunk[:chunk.index(">")] + "<" + chunk[
chunk.index(">") + 1:] #Signal last chunk
print("Generating QRCode for chunk " + str(counter) + ", " +
(str(len(b85Content)) if b85Content else "0") +
" bytes remaining")
qrCode = QRencode(chunk)
#Used for debugging
if args.plainChunk:
f = open("chunk" + str(counter) + ".chunk", "w")
f.write(chunk)
f.close
if counter % 6 == 0:
pdfPage = page(canvas(), paperformat=paperformat.A4, centered=0)
pdf.append(pdfPage)
pdfPage.canvas.insert(
bitmap(**pdfImagePlacement(counter), image=qrCode.convert("LA")))
if args.makeBmp:
qrCode.save("chunk" + str(counter) + ".bmp")
counter += 1
print("Writing to pdf...")
outFile = Path(args.output)
if (outFile.suffix == ".pdf"):
pdf.writePDFfile(args.output)
else:
pdf.writePDFfile(args.output + ".pdf")
print("Done")
def make_dirs_plot(filename, dirs_dict, other=None):
plot_canvas = canvas.canvas()
plot_canvas.stroke(path.circle(0, 0, 10))
for sample_name in dirs_dict.keys():
if other is None:
dirs_dict[sample_name].plot(plot_canvas)
else:
dirs_dict[sample_name].plot(plot_canvas, other=other[sample_name])
plot_canvas.writePDFfile(filename)
def client(clientcolor=color.rgb(0.8, 0.5, 0.5)):
c = canvas.canvas()
r = 0.3
c.fill(path.circle(0, 0, r), [clientcolor])
r = 0.5
p = path.path(path.moveto(-r, 0), path.curveto(-r, r, r, r, r, 0),
path.closepath())
c.fill(p, [clientcolor, trafo.translate(0, -1.3 * r)])
return c
def server(r, servercolor=color.rgb(0.5, 0.5, 0.8)):
c = canvas.canvas()
c.fill(path.circle(0, 0, r), [servercolor, trafo.scale(1, 0.5)])
h = 2 * r
p = path.path(path.moveto(-r, 0), path.lineto(-r, -h),
path.arc(0, -h, r, 180, 0), path.lineto(r, 0),
path.arcn(0, 0, r, 0, 180), path.closepath())
c.fill(p, [servercolor, trafo.scale(1, 0.5).translated(0, -0.08 * r)])
return c
def repo(label, colorfg, colorbg):
crepo = canvas.canvas()
labeltext = text.text(0, 0, r'\textsf{{{}}}'.format(label),
[colorfg])
extrawd = 0.15
labelbox = labeltext.bbox().enlarged(extrawd)
crepo.fill(labelbox.path(), [colorbg, deformer.smoothed(0.05),
deco.stroked([colorfg])])
crepo.insert(labeltext)
return crepo
def plot_key(width, height):
c = canvas.canvas()
w = height / 7.0
for i, meth in enumerate(methods):
c.fill(path.rect(1.0, (6 - i) * w - 0.1, 0.2, 0.2),
[method_colors[meth]])
c.text(1.3, (6 - i) * w, "%s" % meth_names[meth],
[text.halign.left, text.valign.middle,
text.size(-3)])
return c
def read(size, color):
size = size * 0.25
cread = canvas.canvas()
cread.fill(path.circle(0, 0, 0.35), [color, trafo.scale(size)])
p = path.path(path.moveto(0.8, 0),
path.curveto(0.2, 0.5, -0.2, 0.5, -0.8, 0),
path.curveto(-0.2, -0.5, 0.2, -0.5, 0.8, 0),
path.closepath())
cread.stroke(p, [color, style.linewidth.thick, trafo.scale(size)])
return cread
def plot_key(width, height, data):
methods = data.keys()
methods.sort()
c = canvas.canvas()
step = height / float(len(method_colors))
for i, meth in enumerate(methods):
c.fill(path.rect(0.2, height - step * (i + 0.5) - 0.1, 0.2, 0.2),
[method_colors[meth]])
c.text(0.5, height - step * (i + 0.5), meth, [text.halign.left, text.valign.middle, text.size(-2)])
return c
def main():
out_fname = sys.argv[1]
basedir = '/'.join(os.path.dirname(os.path.realpath(__file__)).split('/')[:-2])
hic_fname1 = "%s/Data/HiC/HiFive/mm9_ESC_NcoI_prob.hcp" % basedir
hic_fname2 = "%s/Data/HiC/HiFive/mm9_ESC_HindIII_prob.hcp" % basedir
fivec_fnames = {
"Prob_Phillips":"%s/Data/FiveC/HiFive/Phillips_ESC_prob.fcp" % basedir,
"Prob_Nora":"%s/Data/FiveC/HiFive/Nora_ESC_male_E14_prob.fcp" % basedir,
"Bin_Phillips":"%s/Data/FiveC/HiFive/Phillips_ESC_bin.fcp" % basedir,
"Bin_Nora":"%s/Data/FiveC/HiFive/Nora_ESC_male_E14_bin.fcp" % basedir,
"Exp_Phillips":"%s/Data/FiveC/HiFive/Phillips_ESC_exp.fcp" % basedir,
"Exp_Nora":"%s/Data/FiveC/HiFive/Nora_ESC_male_E14_exp.fcp" % basedir,
"Exp-KR_Phillips":"%s/Data/FiveC/HiFive/Phillips_ESC_expKR.fcp" % basedir,
"Exp-KR_Nora":"%s/Data/FiveC/HiFive/Nora_ESC_male_E14_expKR.fcp" % basedir,
}
hic1 = hifive.HiC(hic_fname1)
hic2 = hifive.HiC(hic_fname2)
hic_hm = { 'Phillips': {} }
fc = hifive.FiveC(fivec_fnames["Prob_Phillips"])
fragments = fc.frags['fragments'][...]
regions = fc.frags['regions'][...]
for i in range(fc.frags['regions'].shape[0]):
binbounds = numpy.hstack((
fragments['start'][regions['start_frag'][i]:regions['stop_frag'][i]].reshape(-1, 1),
fragments['stop'][regions['start_frag'][i]:regions['stop_frag'][i]].reshape(-1, 1)))
binbounds = binbounds[numpy.where(fc.filter[regions['start_frag'][i]:regions['stop_frag'][i]])[0], :]
hic_hm['Phillips'][i] = dynamically_bin(hic1, hic2, regions['chromosome'][i], binbounds)
fc = hifive.FiveC(fivec_fnames["Prob_Nora"])
fragments = fc.frags['fragments'][...]
regions = fc.frags['regions'][...]
binbounds = numpy.hstack((
fragments['start'][regions['start_frag'][0]:regions['stop_frag'][0]].reshape(-1, 1),
fragments['stop'][regions['start_frag'][0]:regions['stop_frag'][0]].reshape(-1, 1)))
binbounds = binbounds[numpy.where(fc.filter[regions['start_frag'][0]:regions['stop_frag'][0]])[0], :]
hic_hm['Nora'] = dynamically_bin(hic1, hic2, regions['chromosome'][0], binbounds)
dist_corr = find_correlations( hic_hm, fivec_fnames, out_fname, True )
nodist_corr = find_correlations( hic_hm, fivec_fnames, out_fname, False )
c = canvas.canvas()
width = 16.8
spacer = 0.4
plot_width = (width - spacer * 2) / 2.5
plot_height = plot_width
key_width = width - (plot_width + spacer) * 2
phillips_img = plot_correlation_diffs(dist_corr, nodist_corr, 'Phillips', plot_width, plot_height)
nora_img = plot_correlation_diffs(dist_corr, nodist_corr, 'Nora', plot_width, plot_height)
key_img = plot_key(key_width, plot_height)
c.insert(phillips_img)
c.insert(nora_img, [trafo.translate(plot_width + spacer, 0)])
c.insert(key_img, [trafo.translate((plot_width + spacer) * 2, 0)])
c.text(0, plot_height, "a",
[text.halign.left, text.valign.top, text.size(-1)])
c.text(plot_width + spacer, plot_height, "b",
[text.halign.left, text.valign.top, text.size(-1)])
c.writePDFfile(out_fname)
def processPDF(self, file, writer, context, registry, bbox):
if writer.mesh_as_bitmap:
from pyx import bitmap, canvas
import Image
c = canvas.canvas()
c.insert(self)
fd, fname = tempfile.mkstemp()
f = os.fdopen(fd, "wb")
f.close()
c.pipeGS(fname,
device="pngalpha",
resolution=writer.mesh_as_bitmap_resolution)
i = Image.open(fname)
os.unlink(fname)
b = bitmap.bitmap_pt(self.bbox().llx_pt, self.bbox().lly_pt, i)
# we slightly shift the bitmap to re-center it, as the bitmap might contain some additional border
# unfortunately we need to construct another bitmap instance for that ...
b = bitmap.bitmap_pt(
self.bbox().llx_pt + 0.5 *
(self.bbox().width_pt() - b.bbox().width_pt()),
self.bbox().lly_pt + 0.5 *
(self.bbox().height_pt() - b.bbox().height_pt()), i)
b.processPDF(file, writer, context, registry, bbox)
else:
thisbbox = self.bbox()
bbox += thisbbox
d = self.data(thisbbox)
if writer.compress:
filter = "/Filter /FlateDecode\n"
d = zlib.compress(d)
else:
filter = ""
name = "shading-%s" % id(self)
shading = PDFGenericResource(
"shading", name, """<<
/ShadingType 4
/ColorSpace %s
/BitsPerCoordinate 24
/BitsPerComponent 8
/BitsPerFlag 8
/Decode [%f %f %f %f %s]
/Length %i
%s>>
stream
%s
endstream\n""" % (self.elements[0].nodes[0].value.colorspacestring(),
thisbbox.llx_pt, thisbbox.urx_pt, thisbbox.lly_pt,
thisbbox.ury_pt, " ".join([
"0 1" for value in
self.elements[0].nodes[0].value.to8bitstring()
]), len(d), filter, d))
registry.add(shading)
registry.addresource("Shading", name, shading)
file.write("/%s sh\n" % name)
def plot_key(width, height):
c = canvas.canvas()
step = height / float(len(method_colors))
for i, meth in enumerate(
['HiFive-Probability', 'HiFive-Express', 'HiFive-Binning']):
c.fill(path.rect(0.2, height - step * (i + 0.5) - 0.1, 0.2, 0.2),
[method_colors[meth]])
c.text(0.5, height - step * (i + 0.5), meth,
[text.halign.left, text.valign.middle,
text.size(-2)])
return c
def main():
# set up the line tracing function
tracer = sunburst.Trace(
os.path.dirname(os.path.abspath(sunburst.__file__)),
sunburst.generate_diagrams, sunburst.stop_trace)
sys.settrace(tracer.trace)
# where is the sunburst directory?
path = os.path.dirname(os.path.abspath(sunburst.__file__))
# instantiate canvases
shape_canvas = canvas.canvas()
text_canvas = canvas.canvas()
# read in settings
settings = yaml.load(open('config.yaml', 'r'))
# list of diagrams to create
data = [('test', (0, 0), ('raw', )),
('test2', (settings['output']['xdelta'], 0), ('trace',
tracer.lines))]
sunburst.generate_diagrams(data, shape_canvas, text_canvas, settings, path)
sunburst.output(settings['output']['name'], shape_canvas, text_canvas)
print(tracer.traced)
def build_canvas():
cnv = canvas.canvas()
cnv.stroke(make_line(w), [deco.earrow()])
text_at(cnv, w / 2. - (.5, 0), r'$\vec{w}$')
cnv.stroke(make_line(v), [deco.earrow()])
text_at(cnv, v / 2. - (0, .5), r'$\vec{v}$')
cnv.stroke(make_line(w, c * v), [deco.earrow(), rgb.red])
text_at(cnv, w - (w - c * v) / 2 + (.1, .1), r'$\vec{w} - c \vec{v}$')
cnv.stroke(make_line(c * v), [deco.earrow(), ls.dashed, rgb.blue])
text_at(cnv, c * v / 1.5 - (0, .5), r'$c \vec{v}$')
cnv.stroke(make_line(v * -1.5, v * 3), [ls.dotted])
return cnv
def draw_points(points: torch.Tensor, filename, size=1, svg=False):
c = canvas.canvas()
points = points.detach().cpu()
for i in range(points.shape[0]):
c.fill(path.circle(points[i, 1], -points[i, 0], size))
if svg:
c.writeSVGfile(file=filename)
else:
c.writePDFfile(file=filename)
def axisatv(self, axis, v):
if axis.positioner.fixtickdirection[0]:
# it is a y-axis
t = trafo.translate_pt(self.xpos_pt + v*self.width_pt - axis.positioner.x1_pt, 0)
else:
# it is an x-axis
t = trafo.translate_pt(0, self.ypos_pt + v*self.height_pt - axis.positioner.y1_pt)
c = canvas.canvas()
for layer, subcanvas in axis.canvas.layers.items():
c.layer(layer).insert(subcanvas, [t])
assert len(axis.canvas.layers) == len(axis.canvas.items), str(axis.canvas.items)
axis.canvas = c
def checkone(knots, refpoints): # <<<
print(myprint(knots))
mp_make_choices(knots, epsilon)
print(myprint(knots))
c = canvas.canvas()
c.stroke(mypath(knots), [deco.shownormpath(), deco.earrow.normal])
c.writePDFfile(bboxenlarge=unit.t_cm)
c.writeEPSfile(bboxenlarge=unit.t_cm)
c.writeSVGfile(bboxenlarge=unit.t_cm)
check(knots, refpoints)
def checkone(knots, refpoints): # <<<
print(myprint(knots))
mp_make_choices(knots, epsilon)
print(myprint(knots))
c = canvas.canvas()
c.stroke(mypath(knots), [deco.shownormpath(), deco.earrow.normal])
c.writePDFfile(bboxenlarge=unit.t_cm)
c.writeEPSfile(bboxenlarge=unit.t_cm)
c.writeSVGfile(bboxenlarge=unit.t_cm)
check(knots, refpoints)
def __init__(self, nsquares):
self.nsquares = nsquares
self.corners = deque([
np.array([0, 0]),
np.array([1, 0]),
np.array([1, 1]),
np.array([0, 1])
])
self.counter = 1
self.initialize_pyx()
self.c = canvas.canvas()
self.draw()
def checkall(): # <<<
c = None
for knots, refpoints in [curve1(), curve2(), curve3(),
curve4(-90), curve4(0), curve4(70), curve5(),
curve6a(), curve6b(), curve6c(), curve7(),
curve8a(), curve8b(), curve9(), curve10()]:
#print myprint(knots)
mp_make_choices(knots, epsilon)
#print myprint(knots)
cc = canvas.canvas()
cc.stroke(mypath(knots), [deco.shownormpath(), deco.earrow.normal])
if c is None:
c = canvas.canvas()
c.insert(cc)
else:
c.insert(cc, [trafo.translate(0, c.bbox().bottom() - cc.bbox().top()-0.5)])
check(knots, refpoints)
c.writePDFfile()
c.writeEPSfile()
c.writeSVGfile()
def write(size, color):
size = size * 0.3
cwrite = canvas.canvas()
p = path.path(path.moveto(-0.2, 0.8), path.lineto(0.2, 0.8),
path.lineto(0.2, 0), path.lineto(0, -0.2),
path.lineto(-0.2, 0), path.lineto(-0.2, 0.8),
path.closepath(), path.moveto(0, 0.8), path.lineto(0, 0.05),
path.moveto(-0.2, 0), path.arcn(-0.1, 0, 0.1, 180, 20),
path.arcn(0.1, 0, 0.1, 160, 0))
cwrite.stroke(
p, [color,
trafo.scale(size).rotated(-30).translated(0, -0.4 * size)])
return cwrite
def processSVG(self, xml, writer, context, registry, bbox):
from pyx import bitmap, canvas
from PIL import Image
c = canvas.canvas()
c.insert(self)
i = Image.open(c.pipeGS("pngalpha", resolution=writer.mesh_as_bitmap_resolution))
i.load()
b = bitmap.bitmap_pt(self.bbox().llx_pt, self.bbox().lly_pt, i)
# we slightly shift the bitmap to re-center it, as the bitmap might contain some additional border
# unfortunately we need to construct another bitmap instance for that ...
b = bitmap.bitmap_pt(self.bbox().llx_pt + 0.5*(self.bbox().width_pt()-b.bbox().width_pt()),
self.bbox().lly_pt + 0.5*(self.bbox().height_pt()-b.bbox().height_pt()), i)
b.processSVG(xml, writer, context, registry, bbox)
def processPDF(self, file, writer, context, registry, bbox):
warnings.warn("EPS file is included as a bitmap created using pipeGS")
from pyx import bitmap, canvas
import Image
c = canvas.canvas()
c.insert(self)
i = Image.open(c.pipeGS(device="pngalpha", resolution=600, seekable=True))
i.load()
b = bitmap.bitmap_pt(self.bbox().llx_pt, self.bbox().lly_pt, i)
# we slightly shift the bitmap to re-center it, as the bitmap might contain some additional border
# unfortunately we need to construct another bitmap instance for that ...
b = bitmap.bitmap_pt(self.bbox().llx_pt + 0.5*(self.bbox().width_pt()-b.bbox().width_pt()),
self.bbox().lly_pt + 0.5*(self.bbox().height_pt()-b.bbox().height_pt()), i)
b.processPDF(file, writer, context, registry, bbox)
def plot_overall(data, width, height, name):
vo = 0.55
ho = 0.7
plot_width = width - ho
plot_height = height - vo - 0.3
c = canvas.canvas()
methods = data.keys()
methods.sort()
bar_colors = []
cis_binsizes = numpy.unique(data[methods[0]]['binsize'][numpy.where(data[methods[0]]['interaction'] == 'cis')])
trans_binsizes = numpy.unique(data[methods[0]]['binsize'][numpy.where(data[methods[0]]['interaction'] == 'trans')])
Y = numpy.zeros((len(methods), cis_binsizes.shape[0] + trans_binsizes.shape[0]), dtype=numpy.float32)
for i, method in enumerate(methods):
for j, binsize in enumerate(cis_binsizes):
where = numpy.where((data[method]['binsize'] == binsize) *
(data[method]['interaction'] == 'cis') *
(data[method]['range'] == 0))
if where[0].shape[0] > 0:
Y[i, j] = data[method]['correlation'][where]
for j, binsize in enumerate(trans_binsizes):
where = numpy.where((data[method]['binsize'] == binsize) *
(data[method]['interaction'] == 'trans') *
(data[method]['range'] == 0))
if where[0].shape[0] > 0:
Y[i, j + cis_binsizes.shape[0]] = data[method]['correlation'][where]
bar_colors.append(method_colors[method])
Y = numpy.array(Y)
g = graph.graphxy(width=plot_width, height=plot_height,
x=graph.axis.nestedbar(painter=graph.axis.painter.bar(nameattrs=None)),
y=graph.axis.lin(painter=painter),
x2=graph.axis.lin(parter=None, min=0, max=1),
y2=graph.axis.lin(parter=None, min=0, max=1))
for i in range(len(methods)):
g.plot(graph.data.points(zip(zip(range(Y.shape[1]), [i] * Y.shape[1]), Y[i, :]), xname=1, y=2),
[graph.style.changebar([method_colors[methods[i]]])])
c.insert(g, [trafo.translate(ho, vo)])
for i, label in enumerate(["10Kb", "50Kb", "250Kb", "1Mb", "250Kb", "1Mb"]):
c.text(ho + plot_width * (i + 0.5) / 6.0, vo - 0.05, "%s" % label,
[text.halign.center, text.valign.top, text.size(-3)])
c.text(ho + plot_width * 2.0 / 6.0, 0.05, "cis",
[text.halign.center, text.valign.bottom, text.size(-3)])
c.stroke(path.line(ho + 0.2, vo * 0.5, ho - 0.2 + plot_width * 4.0 / 6.0, vo * 0.5), [style.linewidth.THin])
c.text(ho + plot_width * 5.0 / 6.0, 0.05, "trans",
[text.halign.center, text.valign.bottom, text.size(-3)])
c.stroke(path.line(ho + 0.2 + plot_width * 4.0 / 6.0, vo * 0.5, ho - 0.2 + plot_width, vo * 0.5), [style.linewidth.THin])
c.text(0, plot_height * 0.5 + vo, "Correlation",
[text.halign.center, text.valign.top, text.size(-3), trafo.rotate(90)])
c.text(plot_width * 0.5 + ho, height, name,
[text.halign.center, text.valign.top, text.size(-3)])
return c
def plot_overall(data, width, height, int_type):
methods = data.keys()
methods.sort()
vo = 0.3
ho = 0.8
plot_width = width - ho
plot_height = height - vo - 0.3
c = canvas.canvas()
bar_colors = []
binsizes = numpy.unique(data[methods[0]]['binsize'][numpy.where(data[methods[0]]['interaction'] == int_type)])
Y = numpy.zeros((len(methods), binsizes.shape[0]), dtype=numpy.float32)
for i, method in enumerate(methods):
for j, binsize in enumerate(binsizes):
where = numpy.where((data[method]['binsize'] == binsize) *
(data[method]['interaction'] == int_type) *
(data[method]['range'] == 0))
if where[0].shape[0] > 0:
Y[i, j] = data[method]['correlation'][where]
bar_colors.append(method_colors[method])
Y = numpy.array(Y)
minY = numpy.amin(Y)
maxY = numpy.amax(Y)
spanY = maxY - minY
minY -= spanY * 0.05
maxY += spanY * 0.05
g = graph.graphxy(width=plot_width, height=plot_height,
x=graph.axis.nestedbar(painter=graph.axis.painter.bar(nameattrs=None)),
y=graph.axis.lin(painter=painter, min=minY, max=maxY),
x2=graph.axis.lin(parter=None, min=0, max=1),
y2=graph.axis.lin(parter=None, min=0, max=1))
for i in range(len(methods)):
g.plot(graph.data.points(zip(zip(range(Y.shape[1]), [i] * Y.shape[1]), Y[i, :]), xname=1, y=2),
[graph.style.changebar([method_colors[methods[i]]])])
c.insert(g, [trafo.translate(ho, vo)])
if int_type == 'cis':
for i, label in enumerate(["10Kb", "50Kb", "250Kb", "1Mb"]):
c.text(ho + plot_width * (i + 0.5) / 4.0, vo - 0.05, "%s" % label,
[text.halign.center, text.valign.top, text.size(-3)])
c.text(ho + plot_width * 0.5, height, "Cis",
[text.halign.center, text.valign.top, text.size(-2)])
else:
for i, label in enumerate(["250Kb", "1Mb"]):
c.text(ho + plot_width * (i + 0.5) / 2.0, vo - 0.05, "%s" % label,
[text.halign.center, text.valign.top, text.size(-3)])
c.text(ho + plot_width * 0.5, height, "Trans",
[text.halign.center, text.valign.top, text.size(-2)])
c.text(0, plot_height * 0.5 + vo, "Correlation",
[text.halign.center, text.valign.top, text.size(-3), trafo.rotate(90)])
return c
def processPDF(self, file, writer, context, registry, bbox):
if writer.mesh_as_bitmap:
from pyx import bitmap, canvas
import Image
c = canvas.canvas()
c.insert(self)
fd, fname = tempfile.mkstemp()
f = os.fdopen(fd, "wb")
f.close()
c.pipeGS(fname, device="pngalpha", resolution=writer.mesh_as_bitmap_resolution)
i = Image.open(fname)
os.unlink(fname)
b = bitmap.bitmap_pt(self.bbox().llx_pt, self.bbox().lly_pt, i)
# we slightly shift the bitmap to re-center it, as the bitmap might contain some additional border
# unfortunately we need to construct another bitmap instance for that ...
b = bitmap.bitmap_pt(self.bbox().llx_pt + 0.5*(self.bbox().width_pt()-b.bbox().width_pt()),
self.bbox().lly_pt + 0.5*(self.bbox().height_pt()-b.bbox().height_pt()), i)
b.processPDF(file, writer, context, registry, bbox)
else:
thisbbox = self.bbox()
bbox += thisbbox
d = self.data(thisbbox)
if writer.compress:
filter = "/Filter /FlateDecode\n"
d = zlib.compress(d)
else:
filter = ""
name = "shading-%s" % id(self)
shading = PDFGenericResource("shading", name, """<<
/ShadingType 4
/ColorSpace %s
/BitsPerCoordinate 24
/BitsPerComponent 8
/BitsPerFlag 8
/Decode [%f %f %f %f %s]
/Length %i
%s>>
stream
%s
endstream\n""" % (self.elements[0].nodes[0].value.colorspacestring(),
thisbbox.llx_pt, thisbbox.urx_pt, thisbbox.lly_pt, thisbbox.ury_pt,
" ".join(["0 1" for value in self.elements[0].nodes[0].value.to8bitstring()]),
len(d), filter, d))
registry.add(shading)
registry.addresource("Shading", name, shading)
file.write("/%s sh\n" % name)
def main():
out_fname = sys.argv[1]
basedir = '/'.join(os.path.dirname(os.path.realpath(__file__)).split('/')[:-2])
bin_file = '%s/Analysis/hifive_mm9_ESC_prob_correlations.txt' % basedir
pois_file = '%s/Analysis/hifive_mm9_ESC_probpois_correlations.txt' % basedir
bin_data = load_data(bin_file)
pois_data = load_data(pois_file)
width = 16.8
spacer = 0.4
range_width = (width - spacer) / 5.0
range_height = range_width * 1.4
c = canvas.canvas()
ranges_img = plot_dataset_ranges(bin_data, pois_data, range_width * 4, range_height)
c.insert(ranges_img)
overall_img = plot_overall(bin_data, pois_data, range_width, range_height)
c.insert(overall_img, [trafo.translate(range_width * 4 + spacer, 0)])
c.writePDFfile(out_fname)
def matrix_22(m, dx=0.5, dy=0.5, pd=0.1, pdx=0.1, pdy=0.3):
c = canvas.canvas()
for nx in range(2):
for ny in range(2):
c.text(nx*dx, -ny*dy, str(m[ny, nx]), [text.halign.center])
box = c.bbox()
xoff = box.left()-pd
c.stroke(path.curve(xoff, box.top()+pd,
xoff-pdx, box.top()-pdy,
xoff-pdx, box.bottom()+pdy,
xoff, box.bottom()-pd))
xoff = box.right()+pd
c.stroke(path.curve(xoff, box.top()+pd,
xoff+pdx, box.top()-pdy,
xoff+pdx, box.bottom()+pdy,
xoff, box.bottom()-pd))
return c
def main():
out_fname = sys.argv[1]
basedir = '/'.join(os.path.dirname(os.path.realpath(__file__)).split('/')[:-2])
mm9_methods = {
'HiFive-Probability':'%s/Analysis/hifive_mm9_ESC_prob_correlations.txt' % basedir,
'HiFive-Express':'%s/Analysis/hifive_mm9_ESC_exp_correlations.txt' % basedir,
'HiFive-Binning':'%s/Analysis/hifive_mm9_ESC_bin_correlations.txt' % basedir,
'HiCNorm':'%s/Analysis/hicnorm_mm9_ESC_correlations.txt' % basedir,
'HiCPipe':'%s/Analysis/hicpipe_mm9_ESC_correlations.txt' % basedir,
'Matrix-Balancing':'%s/Analysis/mb_mm9_ESC_correlations.txt' % basedir,
}
hg19_methods = {
'HiFive-Probability':'%s/Analysis/hifive_hg19_GM12878_prob_correlations.txt' % basedir,
'HiFive-Express':'%s/Analysis/hifive_hg19_GM12878_exp_correlations.txt' % basedir,
'HiFive-Binning':'%s/Analysis/hifive_hg19_GM12878_bin_correlations.txt' % basedir,
'HiCNorm':'%s/Analysis/hicnorm_hg19_GM12878_correlations.txt' % basedir,
'HiCPipe':'%s/Analysis/hicpipe_hg19_GM12878_correlations.txt' % basedir,
'Matrix-Balancing':'%s/Analysis/mb_hg19_GM12878_correlations.txt' % basedir,
}
mm9_data = load_data(mm9_methods)
hg19_data = load_data(hg19_methods)
width = 16.8
spacer = 0.4
overall_width = (width - spacer * 2) / 2.6
c = canvas.canvas()
mm9_ranges_img, mm9_ranges_height = plot_dataset_ranges(mm9_data, width, "MM9 ESC")
mm9_ranges_img.text(0, mm9_ranges_height, 'a',
[text.halign.left, text.valign.top, text.size(-1)])
c.insert(mm9_ranges_img)
hg19_ranges_img, hg19_ranges_height = plot_dataset_ranges(hg19_data, width, "HG19 GM12878")
hg19_ranges_img.text(0, hg19_ranges_height, 'b',
[text.halign.left, text.valign.top, text.size(-1)])
c.insert(hg19_ranges_img, [trafo.translate(0, -hg19_ranges_height - spacer)])
overall_height = mm9_ranges_height * 0.6
mm9_overall_img = plot_overall(mm9_data, overall_width, overall_height, "MM9 ESC")
mm9_overall_img.text(0, overall_height + 0.1, 'c',
[text.halign.left, text.valign.top, text.size(-1)])
c.insert(mm9_overall_img, [trafo.translate(0, -hg19_ranges_height - overall_height - spacer * 2)])
hg19_overall_img = plot_overall(hg19_data, overall_width, overall_height, "HG19 GM12878")
hg19_overall_img.text(0, overall_height + 0.1, 'd',
[text.halign.left, text.valign.top, text.size(-1)])
c.insert(hg19_overall_img, [trafo.translate(overall_width * 1.6 + spacer * 2,
-hg19_ranges_height - overall_height - spacer * 2)])
c.insert(plot_key(overall_width * 0.6 + 0.4, overall_height),
[trafo.translate(overall_width + spacer + 0.6, -hg19_ranges_height - overall_height - spacer * 2)])
c.writePDFfile(out_fname)
def plot_single_range(data, binsize, width, height):
plot_width = width
plot_height = height
c = canvas.canvas()
xmax = 0.0
methods = data.keys()
methods.sort()
for method in methods:
where = numpy.where((data[method]['binsize'] == binsize) *
(data[method]['interaction'] == 'cis') *
(data[method]['range'] > 0))
if where[0].shape[0] > 0:
xmax = max(xmax, numpy.amax(data[method]['range'][where]))
X = data[method]['range'][where]
X = numpy.r_[0, X]
X[0] = X[1] ** 2.0 / X[2]
xmin = X[0]
g = graph.graphxy(width=plot_width, height=plot_height,
x=graph.axis.log(painter=painter, min=X[0], max=xmax),
y=graph.axis.lin(painter=painter),
x2=graph.axis.lin(parter=None, min=0, max=1),
y2=graph.axis.lin(parter=None, min=0, max=1))
for x in X[1:-1]:
pos = ((log(x) - log(xmin)) / (log(xmax) - log(xmin)) * plot_width)
g.stroke(path.line(pos, 0, pos, plot_height), [style.linestyle.dotted, style.linewidth.THin])
X = (X[1:] ** 0.5) * (X[:-1] ** 0.5)
for method in methods:
where = numpy.where((data[method]['binsize'] == binsize) *
(data[method]['interaction'] == 'cis') *
(data[method]['range'] > 0))
if where[0].shape[0] > 0:
Y = data[method]['correlation'][where]
g.plot(graph.data.points(zip(X, Y), x=1, y=2),
[graph.style.line(lineattrs=[method_colors[method], style.linewidth.Thick])])
if binsize / 1000000 > 0:
binstring = "%iMb" % (binsize / 1000000)
elif binsize / 1000 > 0:
binstring = "%iKb" % (binsize / 1000)
else:
binstring = str(binsize)
g.text(plot_width / 2, plot_height + 0.3, "%s binning" % (binstring),
[text.halign.center, text.valign.top, text.size(-2)])
c.insert(g)
return c