def test_empty_drawing(self):
dwg = Drawing(profile="tiny")
result = dwg.tostring()
self.assertEqual(result, '<svg baseProfile="tiny" height="100%" version="1.2" '\
'width="100%" xmlns="http://www.w3.org/2000/svg" '\
'xmlns:ev="http://www.w3.org/2001/xml-events" '\
'xmlns:xlink="http://www.w3.org/1999/xlink"><defs /></svg>')
def test_save_as(self):
fn = 'test_drawing.svg'
if os.path.exists(fn):
os.remove(fn)
dwg = Drawing()
dwg.saveas(fn)
self.assertTrue(os.path.exists(fn))
os.remove(fn)
def test_simple_defs(self):
dwg = Drawing()
g = dwg.defs.add(Group(id='test'))
inner_g = g.add(Group(id='innerTest'))
result = dwg.tostring()
self.assertEqual(result, '<svg baseProfile="full" height="100%" version="1.1" '\
'width="100%" xmlns="http://www.w3.org/2000/svg" '\
'xmlns:ev="http://www.w3.org/2001/xml-events" '\
'xmlns:xlink="http://www.w3.org/1999/xlink">' \
'<defs><g id="test"><g id="innerTest" /></g></defs></svg>')
def test_stylesheet(self):
dwg = Drawing()
dwg.add_stylesheet('test.css', 'Test')
f = StringIO()
dwg.write(f)
result = f.getvalue()
f.close()
self.assertEqual(result, '<?xml version="1.0" encoding="utf-8" ?>\n' \
'<?xml-stylesheet href="test.css" type="text/css" title="Test" alternate="no" media="screen"?>\n'
'<svg baseProfile="full" height="100%" version="1.1" width="100%" '\
'xmlns="http://www.w3.org/2000/svg" xmlns:ev="http://www.w3.org/2001/xml-events" '\
'xmlns:xlink="http://www.w3.org/1999/xlink"><defs /></svg>')
def test_non_us_ascii_chars(self):
dwg = Drawing()
dwg.set_desc('öäü')
f = StringIO()
dwg.write(f)
result = f.getvalue()
f.close()
self.assertEqual(result,
'<?xml version="1.0" encoding="utf-8" ?>\n' \
'<svg baseProfile="full" height="100%" version="1.1" width="100%" '\
'xmlns="http://www.w3.org/2000/svg" xmlns:ev="http://www.w3.org/2001/xml-events" '\
'xmlns:xlink="http://www.w3.org/1999/xlink">'
'<title>öäü</title><defs /></svg>')
def new_drawing(filename='plot.svg', display_scale=1): from svgwrite.drawing import Drawing from svgwrite.container import Group size = 2 * PADDING + SCALE dwg = Drawing(filename, size=(size * display_scale, size * display_scale)) dwg.viewbox(minx=0, miny=0, width=size, height=size) add_stylesheet(dwg) canvas = Group(id='canvas') canvas.translate(PADDING, PADDING) canvas.scale(1, -1) canvas.translate(0, -SCALE) dwg.add(canvas) return dwg, canvas
def __init__(self, filename, x_max, y_max, **kwargs):
'''
Initialize this object - you need to pass it a mongo object for it to
operate on.
'''
self.filename = filename
self.x_max = x_max
self.y_max = y_max
if 'x_min' in kwargs:
self.x_min = kwargs['x_min']
else:
self.x_min = 0
if 'y_min' in kwargs:
self.y_min = kwargs['y_min']
else:
self.y_min = 0
if 'height' in kwargs:
self.height = kwargs['height']
else:
self.height = 600
if 'height' in kwargs:
self.height = kwargs['height']
else:
self.height = 1200
if 'debug' in kwargs:
self.debug = kwargs['debug']
else:
self.debug = True
if 'margin_top' in kwargs:
self.margin_top = kwargs['margin_top']
else:
self.margin_top = 20
if 'margin_bottom' in kwargs:
self.margin_bottom = kwargs['margin_bottom']
else:
self.margin_bottom = 20
if 'margin_left' in kwargs:
self.margin_left = kwargs['margin_left']
else:
self.margin_left = 20
if 'margin_right' in kwargs:
self.margin_right = kwargs['margin_right']
else:
self.margin_right = 20
self.max_x = 100
self.max_y_value = 100
self.data = None
# start drawing object
self.plot = Drawing(self.filename, debug = self.debug,
size = (self.height + self.margin_left + self.margin_right, self.height + self.margin_top + self.margin_bottom),
# viewBox = ("0 0 " + str(float(length) + 10) + " " + str(float(width) + 10)),
preserveAspectRatio = "xMinYMin meet") # , size=('200mm', '150mm'), viewBox=('0 0 200 150'))
self.plot.add(Line(start = (self.margin_left - 4, self.margin_top), end = (self.margin_left - 4, self.margin_top + self.height), stroke_width = 0.5, stroke = "black"))
self.plot.add(Line(start = (self.margin_left, self.margin_top + self.height + 4), end = (self.margin_left + self.height, self.margin_top + self.height + 4), stroke_width = 0.5, stroke = "black"))
def test_stylesheet(self):
dwg = Drawing(profile="tiny")
dwg.add_stylesheet('test.css', 'Test')
f = StringIO()
dwg.write(f)
result = f.getvalue()
f.close()
self.assertEqual(
result, '<?xml version="1.0" encoding="utf-8" ?>\n'
'<?xml-stylesheet href="test.css" type="text/css" title="Test" alternate="no" media="screen"?>\n'
'<svg baseProfile="tiny" height="100%" version="1.2" width="100%" '
'xmlns="http://www.w3.org/2000/svg" '
'xmlns:ev="http://www.w3.org/2001/xml-events" '
'xmlns:xlink="http://www.w3.org/1999/xlink"><defs /></svg>')
def set_properties(self, filename, title, start, end, width, height):
'''Set the properties of the canvas on which you'll want to generate your image '''
self.elements = []
self.title = title
self.start = start
self.end = end
self.width = width # default = 200.0
self.height = height # default = 60.0
self.dimension_y = self.height - self.MARGIN - self.BOTTOM_MARGIN # this is the size of the y field
self.dimension_x = self.width - self.MARGIN - self.RIGHT_MARGIN
self.scale_x = float(self.dimension_x) / (self.end - self.start) # this is a scaling variable
self.y_bottom = str(round(self.dimension_y + self.MARGIN, 2))
canvas_size = (str(self.width) + "px" , "100%") # create drawing # Default is 100%,100% - don't override that, as this allows the svg to fit the data and expand as necessary
self.plot = Drawing(filename , size = canvas_size)
background = Rect(insert = (0, 0), size = canvas_size, fill = "white")
self.plot.add(background)
def draw_arrow_w_text_middle(self, scene: Drawing, start: tuple,
point1: tuple, point2: tuple, end: tuple,
height: int, arrowsize: int, is_curved: bool,
text: str, font_size: int, font_family: str,
over: bool, color: tuple):
# Store the appropriate function ouside of the loop
if is_curved:
self._create_curve_arrow(scene, start, point1, point2, end, color)
else:
self._create_rect_arrow(scene, start, point1, point2, end, color)
# Draw arrow
x_coord = (end[0] - arrowsize, end[1] - arrowsize)
z_coord = (end[0] + arrowsize, end[1] - arrowsize)
y_coord = (end[0], end[1])
# Draw the arrow head
scene.add(
Line(x_coord,
y_coord,
shape_rendering='inherit',
stroke=rgb(*color),
stroke_width=1))
scene.add(
Line(z_coord,
y_coord,
shape_rendering='inherit',
stroke=rgb(*color),
stroke_width=1))
direction = 1
if over:
direction = -1
# Write label in the middle under
labelx = min(start[0], point2[0]) + abs(start[0] - point2[0]) // 2
labely = height + direction * font_size # TODO: Should be font height!
scene.add(
Text(text,
insert=(labelx, labely),
fill=rgb(*color),
font_family=font_family,
font_size=font_size,
text_rendering='inherit',
alignment_baseline='central',
text_anchor='middle')
) # TODO: alignment_baseline should be hanging or baseline!
class ScatterPlot(object):
'''A simple scatter diagram plot.'''
def __init__(self, filename, x_max, y_max, **kwargs):
'''
Initialize this object - you need to pass it a mongo object for it to
operate on.
'''
self.filename = filename
self.x_max = x_max
self.y_max = y_max
if 'x_min' in kwargs:
self.x_min = kwargs['x_min']
else:
self.x_min = 0
if 'y_min' in kwargs:
self.y_min = kwargs['y_min']
else:
self.y_min = 0
if 'height' in kwargs:
self.height = kwargs['height']
else:
self.height = 600
if 'height' in kwargs:
self.height = kwargs['height']
else:
self.height = 1200
if 'debug' in kwargs:
self.debug = kwargs['debug']
else:
self.debug = True
if 'margin_top' in kwargs:
self.margin_top = kwargs['margin_top']
else:
self.margin_top = 20
if 'margin_bottom' in kwargs:
self.margin_bottom = kwargs['margin_bottom']
else:
self.margin_bottom = 20
if 'margin_left' in kwargs:
self.margin_left = kwargs['margin_left']
else:
self.margin_left = 20
if 'margin_right' in kwargs:
self.margin_right = kwargs['margin_right']
else:
self.margin_right = 20
self.max_x = 100
self.max_y_value = 100
self.data = None
# start drawing object
self.plot = Drawing(self.filename, debug = self.debug,
size = (self.height + self.margin_left + self.margin_right, self.height + self.margin_top + self.margin_bottom),
# viewBox = ("0 0 " + str(float(length) + 10) + " " + str(float(width) + 10)),
preserveAspectRatio = "xMinYMin meet") # , size=('200mm', '150mm'), viewBox=('0 0 200 150'))
self.plot.add(Line(start = (self.margin_left - 4, self.margin_top), end = (self.margin_left - 4, self.margin_top + self.height), stroke_width = 0.5, stroke = "black"))
self.plot.add(Line(start = (self.margin_left, self.margin_top + self.height + 4), end = (self.margin_left + self.height, self.margin_top + self.height + 4), stroke_width = 0.5, stroke = "black"))
def add_and_zip_data(self, x, y):
'''adds the data to the scatter plot, using zip to asseble the x and y's.'''
self.data = zip(x, y)
def add_data(self, x):
'''adds the data to the scatter plot - no zipping applied.'''
self.data = x
def add_regression(self, slope):
'''place a regression line on the plot.'''
self.max_min()
x = self.max_x
y = slope * x
print "x %f y %f" % (x, y)
if y > self.max_y_value:
y = self.max_y_value
x = y / slope
print "x %f y %f" % (x, y)
self.plot.add(Line(start = (self.margin_left, self.margin_top + self.height),
end = (self.x_to_printx(x), self.y_to_printy(y)),
stroke_width = 1, stroke = "black"))
def x_to_printx(self, x):
'''transforms the x value to an x coordinate'''
return self.margin_left + ((float(x) / self.max_x) * self.height)
def y_to_printy(self, y):
'''transforms the y value to a y coordinate'''
return (self.margin_top + self.height) - ((float(y) / self.max_y_value) * self.height)
def max_min(self):
'''Find Max values for x and y dimensions'''
self.max_x = self.data[0][0]
self.max_y_value = self.data[0][1]
for x, y in self.data:
if x > self.max_x:
self.max_x = x
if y > self.max_y_value:
self.max_y_value = y
print "max x y : %f %f" % (self.max_x, self.max_y_value)
def build(self):
'''assembles the data in the scatterplot, adding the points as circles.'''
self.max_min()
for x, y in self.data:
self.plot.add(Circle(center = (self.margin_left + ((x / self.max_x) * self.height),
(self.margin_top + self.height) - ((y / self.max_y_value) * self.height)),
r = 2, stroke_width = 0.1, stroke_linecap = 'round',
stroke_opacity = 0.3, fill = "dodgerblue",
fill_opacity = 0.2))
self.plot.add(Text(self.max_x, insert = (self.margin_left + self.height - 50, self.margin_top + self.height + 20.0),
fill = "midnightblue", font_size = "15"))
self.data = None
def save(self):
'''save the plot and reset.'''
self.plot.save()
self.plot = None
def to_string(self):
'''convert the plot to string, and reset.'''
z = self.plot.tostring()
self.plot = None
return z
class Histogram(object):
'''
classdocs
'''
def __init__(self, filename, bins, **kwargs):
'''
Initialize this object - you need to pass it a mongo object for it to
operate on.
'''
self.filename = filename
self.bins = bins
self.data_max = 0
self.data_min = 0
self.x_min = 0
if 'x_max' in kwargs:
self.x_max = kwargs['x_max']
else:
self.x_max = 0
if 'x_min' in kwargs:
self.x_min = kwargs['x_min']
else:
self.x_min = 0
if 'gap' in kwargs:
self.gap = kwargs['gap']
else:
self.gap = 5
if 'height' in kwargs:
self.height = kwargs['height']
else:
self.height = 600
if 'height' in kwargs:
self.height = kwargs['height']
else:
self.height = 1200
if 'debug' in kwargs:
self.debug = kwargs['debug']
else:
self.debug = True
if 'margin_top' in kwargs:
self.margin_top = kwargs['margin_top']
else:
self.margin_top = 20
if 'margin_bottom' in kwargs:
self.margin_bottom = kwargs['margin_bottom']
else:
self.margin_bottom = 20
if 'margin_left' in kwargs:
self.margin_left = kwargs['margin_left']
else:
self.margin_left = 20
if 'margin_right' in kwargs:
self.margin_right = kwargs['margin_right']
else:
self.margin_right = 20
self.data = None
self.binned_data = None
# start drawing object
self.plot = Drawing(self.filename, debug = self.debug,
size = (self.height + self.margin_left + self.margin_right,
self.height + self.margin_top + self.margin_bottom),
# viewBox = ("0 0 " + str(float(length) + 10) + " " + str(float(width) + 10)),
preserveAspectRatio = "xMinYMin meet") # , size=('200mm', '150mm'), viewBox=('0 0 200 150'))
self.plot.add(Line(start = (self.margin_left - 4, self.margin_top), \
end = (self.margin_left - 4, self.margin_top + self.height),
stroke_width = 0.5, stroke = "black"))
self.plot.add(Line(start = (self.margin_left, self.margin_top + self.height + 4),
end = (self.margin_left + self.height, self.margin_top + self.height + 4),
stroke_width = 0.5, stroke = "black"))
def add_data(self, x):
self.data = x
def bin_data(self):
self.binned_data = {}
for i in range(self.bins + 1):
self.binned_data[i] = 0
if self.x_max == 0 and self.x_min == 0 :
self.x_min = self.data[0]
for x in self.data:
if x > self.x_max:
self.x_max = x
if x < self.x_min:
self.x_min = x
# print "self.x_max = %f" % (self.x_max)
bin_size = (float(self.x_max) - self.x_min) / self.bins
print "bin_size: %f" % (bin_size)
for x in self.data:
# print "x: %i - bin_size: %f" % (x, bin_size)
# print "x//bin_size = %f int() = %i" % (x // bin_size, int(x // bin_size))
k = 0
if x > self.x_max:
k = self.bins + 1
else:
k = int(x // bin_size)
if k > self.bins:
k = self.bins
self.binned_data[k] += 1 # floored division.
if self.binned_data[k] > self.data_max:
self.data_max = self.binned_data[k]
for i in range(self.bins + 1):
print "%i %i" % (i, self.binned_data[i])
def x_to_printx(self, x):
return self.margin_left + ((float(x) / self.x_max) * self.height)
def build(self):
bin_width = (self.height - ((self.bins + 1) * self.gap)) // self.bins # floored division
for i in range(self.bins):
self.plot.add(Rect(insert = (self.margin_left + self.gap + (i * (bin_width + self.gap)),
(self.margin_top + self.height) - ((float(self.binned_data[i]) / self.data_max) * self.height)),
size = (bin_width, ((float(self.binned_data[i]) / self.data_max) * self.height)),
fill = "red"))
self.plot.add(Text(i , insert = (self.margin_left + self.gap + (i * (bin_width + self.gap)), self.height + self.margin_top + 20), fill = "midnightblue", font_size = "15"))
self.data = None
def save(self):
self.plot.save()
self.plot = None
def to_string(self):
z = self.plot.tostring()
self.plot = None
return z
def get_4cat_canvas(path,
width,
height,
header=None,
footer="made with 4CAT",
fontsize_normal=None,
fontsize_small=None,
fontsize_large=None):
"""
Get a standard SVG canvas to draw 4CAT graphs to
Adds a border, footer, header, and some basic text styling
:param path: The path where the SVG graph will be saved
:param width: Width of the canvas
:param height: Height of the canvas
:param header: Header, if necessary to draw
:param footer: Footer text, if necessary to draw. Defaults to shameless
4CAT advertisement.
:param fontsize_normal: Font size of normal text
:param fontsize_small: Font size of small text (e.g. footer)
:param fontsize_large: Font size of large text (e.g. header)
:return SVG: SVG canvas (via svgwrite) that can be drawn to
"""
from svgwrite.container import SVG
from svgwrite.drawing import Drawing
from svgwrite.shapes import Rect
from svgwrite.text import Text
if fontsize_normal is None:
fontsize_normal = width / 75
if fontsize_small is None:
fontsize_small = width / 100
if fontsize_large is None:
fontsize_large = width / 50
# instantiate with border and white background
canvas = Drawing(str(path),
size=(width, height),
style="font-family:monospace;font-size:%ipx" %
fontsize_normal)
canvas.add(
Rect(insert=(0, 0),
size=(width, height),
stroke="#000",
stroke_width=2,
fill="#FFF"))
# header
if header:
header_shape = SVG(insert=(0, 0), size=("100%", fontsize_large * 2))
header_shape.add(
Rect(insert=(0, 0), size=("100%", "100%"), fill="#000"))
header_shape.add(
Text(insert=("50%", "50%"),
text=header,
dominant_baseline="middle",
text_anchor="middle",
fill="#FFF",
style="font-size:%ipx" % fontsize_large))
canvas.add(header_shape)
# footer (i.e. 4cat banner)
if footer:
footersize = (fontsize_small * len(footer) * 0.7, fontsize_small * 2)
footer_shape = SVG(insert=(width - footersize[0],
height - footersize[1]),
size=footersize)
footer_shape.add(
Rect(insert=(0, 0), size=("100%", "100%"), fill="#000"))
footer_shape.add(
Text(insert=("50%", "50%"),
text=footer,
dominant_baseline="middle",
text_anchor="middle",
fill="#FFF",
style="font-size:%ipx" % fontsize_small))
canvas.add(footer_shape)
return canvas
def _blank_drawing(width: int, height: int) -> Drawing:
base = Drawing(viewBox=f'0 0 {int(width)} {int(height)}', size=(None, None), debug=False, profile='tiny')
return base
def __init__(self,
width=600,
height=400,
margin_top=20,
margin_bottom=40,
margin_left=40,
margin_right=20,
x_min=0,
y_min=None,
x_max=1,
y_max=None,
debug=False,
graph_colour="midnightblue",
background=None,
x_label=None,
y_label=None,
y_label_max_min=True,
title=None):
self.width = width
self.height = height
self.debug = debug
self.margin_top = margin_top
self.margin_bottom = margin_bottom
self.margin_left = margin_left
self.margin_right = margin_right
self.x_max = x_max
self.y_max = y_max
self.x_min = x_min
self.y_min = y_min
self.graph_colour = graph_colour
self.x_label = x_label
self.y_label = y_label
self.y_label_max_min = y_label_max_min
self.title = title
self.font_size = 15
self.plottable_x = self.width - (self.margin_left + self.margin_right)
self.plottable_y = self.height - (self.margin_top + self.margin_bottom)
# start drawing object
self.plot = Drawing(
debug=self.debug,
size=(self.width, self.height),
# viewBox = ("0 0 " + str(float(length) + 10) + " " + str(float(width) + 10)),
preserveAspectRatio="xMinYMin meet"
) # , size=('200mm', '150mm'), viewBox=('0 0 200 150'))
if background:
self.plot.add(
Rect(insert=(0, 0),
size=(self.width, self.height),
fill=background))
if x_label:
self.plottable_y -= self.font_size
self.add_x_label()
if y_label:
self.plottable_x -= self.font_size
self.margin_left += self.font_size
self.add_y_label()
if title:
self.plottable_y -= self.font_size + 5
self.margin_top += self.font_size + 5
self.add_title()
self.plot.add(
Line(start=(self.margin_left - 4, self.margin_top),
end=(self.margin_left - 4,
self.margin_top + self.plottable_y),
stroke_width=1,
stroke=self.graph_colour))
self.plot.add(
Line(start=(self.margin_left,
self.margin_top + self.plottable_y + 4),
end=(self.margin_left + self.plottable_x,
self.margin_top + self.plottable_y + 4),
stroke_width=1,
stroke=self.graph_colour))
if self.y_label_max_min and self.y_max and self.y_min:
self.add_y_max_min(self.y_max, self.y_min)
def make_svg(self, data):
layers = data["layers"]
_PROPORTION = 10
_SHIFT_PROP = _PROPORTION / 1.5
for f in self.forms:
structures = [None] * len(f.id.split("_"))
linkers = []
centers = {}
order = {}
maxW, maxH = 0, 0
for cx, x in enumerate(f.id.split("_")):
order[x] = cx
for cl, l in enumerate(layers):
for cs, s in enumerate(l):
name = f.id + "__" + s["id"]
if s["type"] == "H":
color = "cornflowerblue" if "ref" not in s else "gainsboro"
shape = Circle( center = (s["shift_x"] * _SHIFT_PROP, s["shift_z"] * _SHIFT_PROP),
r = 2.3 * _PROPORTION, id = name,
fill = color, stroke="black",
stroke_width = "2")
elif s["type"] == "E":
color = "indianred" if "ref" not in s else "salmon"
rotate = f.get_ss_by_id(s["id"]).struc.goes_down()
shape = Triangle(center = (s["shift_x"] * _SHIFT_PROP, s["shift_z"] * _SHIFT_PROP),
rc = 2.3 * _PROPORTION, id = name, fill=color,
stroke = "black", stroke_width = "2",
rotate = rotate)
else:
color = "darkgreen" if "ref" not in s else "lightgreen"
shape = Cross(center = (s["shift_x"] * _SHIFT_PROP, s["shift_z"] * _SHIFT_PROP), r = 2.3 * _PROPORTION,
fill=color, stroke="black", stroke_width = "2",
id = name)
structures[order[s["id"]]] = shape
centers[s["id"]] = [s["shift_x"] * _SHIFT_PROP, s["shift_z"] * _SHIFT_PROP]
if s["shift_x"] * _SHIFT_PROP > maxW: maxW = s["shift_x"] * _SHIFT_PROP
if s["shift_z"] * _SHIFT_PROP > maxH: maxH = s["shift_z"] * _SHIFT_PROP
for cx, x in enumerate(f.id.split("_")):
if cx == 0 or cx == len(f.id.split("_")) - 1:
init = [0, 0]
if (ord(x[0]) - 64) <= len(layers) / 2:
init[1] = centers[x][1] - (2.3 * _PROPORTION * 2)
else:
init[1] = centers[x][1] + (2.3 * _PROPORTION * 2)
if int(re.search("(\d+)", x).group(1)) <= len(layers[ord(x[0]) - 65]) / 2:
init[0] = centers[x][0] - (2.3 * _PROPORTION * 2)
else:
init[0] = centers[x][0] + (2.3 * _PROPORTION * 2)
if cx == 0:
shape = Line(init, centers[x], stroke="darkblue", stroke_width = "4")
elif cx == len(f.id.split("_")) - 1:
shape = Line(centers[x], init, stroke="darkred", stroke_width = "4")
linkers.append(shape)
for cy, y in enumerate(f.id.split("_")):
if cy == cx + 1:
shape = Line(centers[x], centers[y], stroke="black", stroke_width = "4")
linkers.append(shape)
# Intercalate
toplink = []
dowlink = []
if f.sslist[0].struc.goes_up():
dowlink = linkers[0:][::2]
toplink = linkers[1:][::2]
else:
dowlink = linkers[1:][::2]
toplink = linkers[0:][::2]
g = Group()
for x in dowlink:
g.add(x)
for x in structures:
g.add(x)
for x in toplink:
g.add(x)
g.translate(2.3 * _PROPORTION * 3, 2.3 * _PROPORTION * 3)
d = Drawing(size = (maxW + ((2.3 * _PROPORTION * 3) * 2),
maxH + ((2.3 * _PROPORTION * 3) * 2)),
id = f.id + "__image")
d.add(g)
for x in data["forms"]:
if x["id"] == f.id:
x["svg"] = d.tostring()
def _func(drawing: Drawing) -> None:
drawing.add(drawing.rect(insert=(x, y), size=(width, height), fill='white'))
def _draw_elements(drawing: Drawing, drawables: List[Drawable]) -> Drawing:
drawing = drawing.copy()
for drawable in drawables:
drawable(drawing)
return drawing
def _func(drawing: Drawing) -> None:
drawing.add(drawing.text(text, (x, y), font_size=size))
def _func(drawing: Drawing) -> None:
drawing.add(drawing.line((x, y), (x_, y_), stroke='black'))
class Plot(object):
"""
Called byrapper object to plot methylation data.
"""
METHYLATION_DOT_RADIUS = 2
METHYLATION_DISTR_HT_MED = 12.0
METHYLATION_DISTR_HT_BIG = 24.0
DISTR_SHIFT = 0
DISTR_STROKE = 0.75
BOTTOM_MARGIN = 120 # 120 pixels
RIGHT_MARGIN = 30
MARGIN = 30
GENE_OFFSET = 20
def __init__(self):
"""Simple initiation of all of the self parameters... Does not do anything unexpected."""
self.elements = []
self.title = None
self.sample_grouping = {} # store sample id/sample group.
self.gausian_colour = {}
self.last_hash = 0
self.start = 0
self.end = 0
self.width = 200 # default = 200.0
self.height = 60 # default = 60.0
self.message = None
self.dimension_y = 0 # this is the size of the y field
self.dimension_x = 0
self.scale_x = 0
self.y_bottom = "0"
self.scale_y = 0
self.maxh = 0
self.plot = None
self.gene_offset = self.GENE_OFFSET
def set_properties(self, filename, title, start, end, width, height):
"""Set the properties of the canvas on which you'll want to generate your image """
self.elements = []
self.title = title
self.start = start
self.end = end
self.width = width # default = 200.0
self.height = height # default = 60.0
self.dimension_y = self.height - self.MARGIN - self.BOTTOM_MARGIN # this is the size of the y field
self.dimension_x = self.width - self.MARGIN - self.RIGHT_MARGIN
self.scale_x = float(self.dimension_x) / (
self.end - self.start) # this is a scaling variable
self.y_bottom = str(round(self.dimension_y + self.MARGIN, 2))
canvas_size = (str(self.width) + "px", "100%")
# create drawing # Default is 100%,100% - don't override that,
# as this allows the svg to fit the data and expand as necessary
self.plot = Drawing(filename, size=canvas_size)
background = Rect(insert=(0, 0), size=canvas_size, fill="white")
self.plot.add(background)
def convert_xcoord_to_pos(self, xcoord):
return round(float(xcoord - self.start) * self.scale_x,
2) + self.MARGIN
def make_gausian(self,
pos,
height,
stddev,
horizontal=True,
y_median=0,
sigmas=3):
""" path points will be at (-3stddev,0), (0,height), (3stddev,0)
Control points at (-1stddev,0), (-1stddev,height), (1stddev,height), (1stddev,0)
"""
x_values = [
-sigmas * stddev, -1 * stddev, -1 * stddev, 0, stddev, stddev,
sigmas * stddev
]
y_values = [0, 0, height, height, height, 0, 0]
if horizontal is True:
x_values = [
round((x - self.start + pos) * self.scale_x, 2) + self.MARGIN
for x in x_values
]
# Scale Y and inverse the coordinates
y_values = [round(y1 * self.scale_y, 2) for y1 in y_values]
y_values = [(self.height - self.BOTTOM_MARGIN - y2)
for y2 in y_values]
else:
switch = [
round(((pos - self.start) * self.scale_x) + y + self.MARGIN +
self.DISTR_SHIFT, 2) for y in y_values
]
y_values = [
round(((x + y_median) * self.scale_y), 2) for x in x_values
]
x_values = switch
d_str = "M " + str(x_values[0]) + "," + str(
y_values[0]) + " C" # point 1
for i in range(1, 7):
d_str += " " + str(x_values[i]) + "," + str(y_values[i])
return d_str
@staticmethod
def filter_waves(waves):
i = 0
while i < len(waves) - 1:
if i > 0: # check if wave is smaller than the last and should be removed
a_pos, a_ht, a_sd = waves[i - 1]
b_pos, b_ht, _b_sd = waves[i]
if b_ht < a_ht and b_pos < a_pos + 3 * a_sd:
waves.pop(i)
continue
if i < len(
waves
) - 2: # check if wave is smaller than the next and should be removed
a_pos, a_ht, _a_sd = waves[i]
b_pos, b_ht, b_sd = waves[i + 1]
if a_ht < b_ht and a_pos < b_pos - 3 * b_sd:
waves.pop(i)
continue
i += 1
return waves
def save(self):
""" push loaded elements to the the plot, clear out the elements. """
for element in self.elements:
self.plot.add(element)
self.elements = None # may want to remove this, if we ever want to do fancy stuff with the elements.
self.plot.save()
def to_string(self):
""" convert the loaded elements to strings and return the list of elements"""
magic_box = Text(" ",
id="sample_name",
insert=((self.MARGIN + 20), (self.MARGIN + 20)),
fill="black",
font_size=MED_FONT)
self.elements.append(magic_box)
t_0 = time.time()
temp = [self.plot.tostring().replace("</svg>", "")]
for element in self.elements:
temp.append(element.tostring())
temp.append("</svg>")
print(f" Conversion of SVG to string took {time.time() - t_0} seconds")
return ''.join(t for t in temp)
def get_xml(self):
""" Convert the loaded elements into XML strings and then return them."""
strings = ""
for element in self.elements:
strings += (element.get_xml().decode('utf-8'))
return strings
def add_legends(self, get_cpg, annotations):
""" Add annotations, title, axis, tic marks and labels """
title = Text(self.title,
insert=(BIG_FONT + ((float(self.MARGIN) - BIG_FONT) / 3),
BIG_FONT + ((float(self.MARGIN) - BIG_FONT) / 3)),
fill=LEGEND_COLOUR,
font_size=BIG_FONT)
self.elements.append(title)
for axis in get_axis(self.width, self.MARGIN, self.height,
self.BOTTOM_MARGIN, self.RIGHT_MARGIN):
self.elements.append(axis)
# print("add_legends, messages are: {}".format(self.message)
if self.message is None:
self.add_xtics()
# self.add_sample_labels(self.width - self.RIGHT_MARGIN + 20)
if get_cpg:
for cpg in add_cpg(annotations, self.MARGIN, self.height,
self.scale_x, self.start, self.end,
self.BOTTOM_MARGIN):
self.elements.insert(0, cpg)
def add_xtics(self):
""" Create X tics on the plot"""
scale_tics = 1
while scale_tics * 10 < self.end - self.start:
scale_tics *= 10
xtics = [
i for i in range(self.start, self.end + 1) if i % scale_tics == 0
]
while len(xtics) < 4:
scale_tics /= 2
xtics += [
j for j in range(self.start, self.end + 1)
if j % scale_tics == 0 and j not in xtics
]
xtics.sort()
spacing = fabs((self.MARGIN + (xtics[1] - self.start) * self.scale_x) -
(self.MARGIN +
(xtics[0] - self.start) * self.scale_x)) / 4
for tic in xtics:
tic_x = (self.MARGIN + (tic - self.start) * self.scale_x)
tic_y = self.height - self.BOTTOM_MARGIN + SMALL_FONT * 1.5
ticmarker = (Text(str(tic),
insert=(tic_x, tic_y),
fill=LEGEND_COLOUR,
font_size=SMALL_FONT))
ticline = Rect(insert=(tic_x,
self.height - self.BOTTOM_MARGIN - 2),
size=(1, 5),
fill=LEGEND_COLOUR)
for i in range(1, 4):
if tic_x - spacing * i > self.MARGIN - 5:
ticline2 = Rect(insert=(tic_x - spacing * i, self.height -
self.BOTTOM_MARGIN - 2),
size=(1, 2),
fill=LEGEND_COLOUR)
self.elements.append(ticline2)
self.elements.append(ticline)
self.elements.append(ticmarker)
def add_ytics_chipseq(self):
""" Add Y ticks to the svg plot """
steps = round(self.maxh / 5, 1) if self.maxh else 1
labels = [0, steps, 2 * steps, 3 * steps, 4 * steps, 5 * steps]
ytics = [
round(
self.height - self.BOTTOM_MARGIN - (self.dimension_y / 5 * y),
3) for y in range(0, 6)
]
spacing = (ytics[0] - ytics[1]) / 2
for tic, label in zip(ytics, labels):
ticline = Rect(insert=(self.MARGIN - 2, tic),
size=(5, 1),
fill=LEGEND_COLOUR)
if tic - spacing > self.MARGIN:
ticline2 = Rect(insert=(self.MARGIN - 2, tic - spacing),
size=(2, 1),
fill=LEGEND_COLOUR)
self.elements.append(ticline2)
tic_x = self.MARGIN - SMALL_FONT * 2
tic_y = tic + 1
if len(str(label)) == 1:
tic_x += 3
if len(str(label)) == 2:
tic_x += 2
if len(str(label)) >= 3:
tic_x -= 10
ticmarker = (Text(str(label),
insert=(tic_x, tic_y),
fill=LEGEND_COLOUR,
font_size=SMALL_FONT))
self.elements.append(ticline)
self.elements.append(ticmarker)
def add_ytics_methylation(self):
""" Add Y ticks to the svg plot """
labels = [0, 0.2, 0.4, 0.6, 0.8, 1]
ytics = [
round((self.MARGIN + self.dimension_y) - (y * self.dimension_y), 3)
for y in labels
]
spacing = (ytics[0] - ytics[1]) / 2
for tic, label in zip(ytics, labels):
ticline = Rect(insert=(self.width - self.RIGHT_MARGIN, tic),
size=(5, 1),
fill=LEGEND_COLOUR)
if tic - spacing > self.MARGIN:
ticline2 = Rect(insert=(self.width - self.RIGHT_MARGIN,
tic - spacing),
size=(2, 1),
fill=LEGEND_COLOUR)
self.elements.append(ticline2)
tic_x = self.width - self.RIGHT_MARGIN + SMALL_FONT
tic_y = tic + 1
if len(str(label)) == 1:
tic_x += 3
if len(str(label)) == 2:
tic_x += 2
ticmarker = (Text(str(label),
insert=(tic_x, tic_y),
fill=LEGEND_COLOUR,
font_size=SMALL_FONT))
self.elements.append(ticline)
self.elements.append(ticmarker)
def draw_genes(self, genes):
for gene in genes:
for transcript in gene['transcripts']:
start = self.convert_xcoord_to_pos(gene['start'])
length = self.convert_xcoord_to_pos(gene['end']) - start
if start < self.MARGIN:
if start < 0: # first, remove anything before zero.
length += start
start = 0
length -= (
self.MARGIN + start
) # then remove anything before the margin begins
start = self.MARGIN
if start + length > (self.width - self.RIGHT_MARGIN):
length = (self.width - self.RIGHT_MARGIN) - start
if gene['strand'] == 1:
text = gene['name'] + " ->>>"
else:
text = " <<<- " + gene['name']
# print "(self.width + self.RIGHT_MARGIN + self.MARGIN)", (self.width - self.RIGHT_MARGIN)
# print "gene -> text:{} chrend:{} chrstart:{} start:{} length:{}"
# .format(gene['name'], gene['end'], gene['start'], start, length)_
g_rect = Rect(insert=(start, self.height - self.BOTTOM_MARGIN +
self.gene_offset + 4),
size=(length, 2),
fill="grey")
g_text = (Text(text,
insert=(start,
self.height - self.BOTTOM_MARGIN +
self.gene_offset + 9),
fill=LEGEND_COLOUR,
font_size=SMALL_FONT))
self.elements.append(g_rect)
self.elements.append(g_text)
for exon in gene["transcripts"][transcript]["exons"]:
exon_info = gene["transcripts"][transcript]["exons"][exon]
e_start = self.convert_xcoord_to_pos(exon_info["start"])
e_len = self.convert_xcoord_to_pos(
exon_info['end']) - e_start
if e_start > (self.width - self.RIGHT_MARGIN) or (
e_start + e_len) < self.MARGIN:
continue
if e_start < self.MARGIN:
e_start = self.MARGIN
if e_start + e_len > (self.width - self.RIGHT_MARGIN):
e_len = (self.width - self.RIGHT_MARGIN) - e_start
e_rect = Rect(insert=(e_start,
self.height - self.BOTTOM_MARGIN +
self.gene_offset),
size=(e_len, 9),
fill="grey")
self.elements.append(e_rect)
self.gene_offset += 12
if self.gene_offset > 250:
self.gene_offset = self.GENE_OFFSET
class Figure(object):
def __init__(self,
width=600,
height=400,
margin_top=20,
margin_bottom=40,
margin_left=40,
margin_right=20,
x_min=0,
y_min=None,
x_max=1,
y_max=None,
debug=False,
graph_colour="midnightblue",
background=None,
x_label=None,
y_label=None,
y_label_max_min=True,
title=None):
self.width = width
self.height = height
self.debug = debug
self.margin_top = margin_top
self.margin_bottom = margin_bottom
self.margin_left = margin_left
self.margin_right = margin_right
self.x_max = x_max
self.y_max = y_max
self.x_min = x_min
self.y_min = y_min
self.graph_colour = graph_colour
self.x_label = x_label
self.y_label = y_label
self.y_label_max_min = y_label_max_min
self.title = title
self.font_size = 15
self.plottable_x = self.width - (self.margin_left + self.margin_right)
self.plottable_y = self.height - (self.margin_top + self.margin_bottom)
# start drawing object
self.plot = Drawing(
debug=self.debug,
size=(self.width, self.height),
# viewBox = ("0 0 " + str(float(length) + 10) + " " + str(float(width) + 10)),
preserveAspectRatio="xMinYMin meet"
) # , size=('200mm', '150mm'), viewBox=('0 0 200 150'))
if background:
self.plot.add(
Rect(insert=(0, 0),
size=(self.width, self.height),
fill=background))
if x_label:
self.plottable_y -= self.font_size
self.add_x_label()
if y_label:
self.plottable_x -= self.font_size
self.margin_left += self.font_size
self.add_y_label()
if title:
self.plottable_y -= self.font_size + 5
self.margin_top += self.font_size + 5
self.add_title()
self.plot.add(
Line(start=(self.margin_left - 4, self.margin_top),
end=(self.margin_left - 4,
self.margin_top + self.plottable_y),
stroke_width=1,
stroke=self.graph_colour))
self.plot.add(
Line(start=(self.margin_left,
self.margin_top + self.plottable_y + 4),
end=(self.margin_left + self.plottable_x,
self.margin_top + self.plottable_y + 4),
stroke_width=1,
stroke=self.graph_colour))
if self.y_label_max_min and self.y_max and self.y_min:
self.add_y_max_min(self.y_max, self.y_min)
def save(self, reset=True, filename=None):
if filename:
self.plot.filename = filename
elif not self.plot.filename:
raise Exception("No Filename set to save SVG image.")
self.plot.save()
print(f"wrote to {self.plot.filename}")
if reset:
self.plot = None
def add_y_label(self):
y_coord = self.margin_top + (self.plottable_y / 2)
text_group = Group(
transform=f"rotate(270, {self.font_size}, {y_coord})")
text_group.add(
Text(self.y_label,
insert=(0, y_coord),
fill=self.graph_colour,
font_size="15",
stroke_width=0))
self.plot.add(text_group)
def add_x_label(self):
self.plot.add(
Text(self.x_label,
insert=(self.plottable_x / 2, self.plottable_y +
self.margin_top + (self.margin_bottom / 2) + 15),
fill=self.graph_colour,
font_size=self.font_size))
def add_title(self):
self.plot.add(
Text(self.title,
insert=(self.plottable_x / 2, self.font_size + 5),
fill=self.graph_colour,
font_size=self.font_size))
def add_y_max_min(self, max_value, min_value):
self.plot.add(
Text(str(round(max_value, 2)),
insert=(self.margin_left - 8, self.margin_top + 15),
text_anchor="end",
fill=self.graph_colour,
font_size=self.font_size))
self.plot.add(
Text(str(min_value),
insert=(self.margin_left - 8,
self.margin_top + self.plottable_y),
text_anchor="end",
fill=self.graph_colour,
font_size=self.font_size))
def add_x_column_labels(self,
column_positions,
column_labels,
rotate=None):
for gene in column_labels:
text_group = Group(
transform=
f"rotate({rotate if rotate else 0},{column_positions[gene]},"
f"{self.margin_top + self.plottable_y + 17})")
text_group.add(
Text(gene,
insert=(column_positions[gene],
self.margin_top + self.plottable_y + 17),
fill=self.graph_colour,
font_size=self.font_size,
stroke_width=0))
self.plot.add(text_group)
def to_string(self, reset=True):
string_value = self.plot.tostring()
if reset:
self.plot = None
return string_value
def add_max_min_text(self):
self.plot.add(
Text(str(self.x_max),
insert=(self.margin_left + self.plottable_x,
self.margin_top + self.plottable_y + 20.0),
text_anchor="end",
fill=self.graph_colour,
font_size=self.font_size))
self.plot.add(
Text(str(self.x_min),
insert=(self.margin_left,
self.margin_top + self.plottable_y + 20.0),
fill=self.graph_colour,
font_size=self.font_size))
self.plot.add(
Text(str(self.y_max),
insert=(self.margin_left - 8, self.margin_top + 10),
text_anchor="end",
fill=self.graph_colour,
font_size=self.font_size))
self.plot.add(
Text(str(self.y_min),
insert=(self.margin_left - 8,
self.margin_top + self.plottable_y),
text_anchor="end",
fill=self.graph_colour,
font_size=self.font_size))
def create_image(filename):
image = Drawing(filename)
image.update({"stroke": "black", "stroke_width": 1})
return image
class Plot(object):
'''
Called by a MongoEpigeneticsWrapper object to plot methylation data.
'''
METHYLATION_DOT_RADIUS = 2
METHYLATION_DISTR_HT_MED = 12.0
METHYLATION_DISTR_HT_BIG = 24.0
DISTR_SHIFT = 0
DISTR_STROKE = 0.75
BOTTOM_MARGIN = 120 # 120 pixels
RIGHT_MARGIN = 30
MARGIN = 30
GENE_OFFSET = 20
palette = Color_Palette.ColorPalette() # APF - reset on each iteration through the sorter.
def __init__(self):
'''Simple initiation of all of the self parameters... Does not do anything unexpected.'''
self.elements = []
self.title = None
self.palette.samples_color = {} # reset the methylation plot colour assignment on initialization.
self.sample_grouping = {} # store sample id/sample group.
self.gausian_colour = {}
self.last_hash = 0
self.start = 0
self.end = 0
self.width = 200 # default = 200.0
self.height = 60 # default = 60.0
self.message = None
self.dimension_y = 0 # this is the size of the y field
self.dimension_x = 0
self.scale_x = 0
self.y_bottom = 0
self.scale_y = 0
self.maxh = 0
self.plot = None
self.gene_offset = self.GENE_OFFSET
def set_properties(self, filename, title, start, end, width, height):
'''Set the properties of the canvas on which you'll want to generate your image '''
self.elements = []
self.title = title
self.start = start
self.end = end
self.width = width # default = 200.0
self.height = height # default = 60.0
self.dimension_y = self.height - self.MARGIN - self.BOTTOM_MARGIN # this is the size of the y field
self.dimension_x = self.width - self.MARGIN - self.RIGHT_MARGIN
self.scale_x = float(self.dimension_x) / (self.end - self.start) # this is a scaling variable
self.y_bottom = str(round(self.dimension_y + self.MARGIN, 2))
canvas_size = (str(self.width) + "px" , "100%") # create drawing # Default is 100%,100% - don't override that, as this allows the svg to fit the data and expand as necessary
self.plot = Drawing(filename , size = canvas_size)
background = Rect(insert = (0, 0), size = canvas_size, fill = "white")
self.plot.add(background)
def set_sample_index(self, types, samples):
'''overwrite the sample_index to preserve colours from previous set.'''
self.palette.set_colors_dict(types, samples)
def get_sample_index(self):
''' Return the sample index so that it can be used in HTML'''
return self.palette.get_colors_dict()
def get_types_index(self):
''' Return the sample index so that it can be used in HTML'''
return self.palette.get_type_colors()
def convert_xcoord_to_pos(self, xcoord):
return round(float(xcoord - self.start) * self.scale_x, 2) + self.MARGIN
def make_gausian(self, pos, height, stddev, horizontal = True, y_median = 0, sigmas = 3):
''' path points will be at (-3stddev,0), (0,height), (3stddev,0)
Control points at (-1stddev,0), (-1stddev,height), (1stddev,height), (1stddev,0)
'''
X = [-sigmas * stddev, -1 * stddev, -1 * stddev, 0, stddev, stddev, sigmas * stddev]
Y = [0, 0, height, height, height, 0, 0]
if horizontal is True:
X = [round((x - self.start + pos) * self.scale_x, 2) + self.MARGIN for x in X]
# Scale Y and inverse the coordinates
Y = [round(y1 * self.scale_y, 2) for y1 in Y]
Y = [(self.height - self.BOTTOM_MARGIN - y2) for y2 in Y]
else:
S = [round(((pos - self.start) * self.scale_x) + y + self.MARGIN + self.DISTR_SHIFT, 2) for y in Y]
Y = [round(((x + y_median) * self.scale_y), 2) for x in X]
X = S
d = "M " + str(X[0]) + "," + str(Y[0]) + " C" # point 1
for i in range(1, 7):
d += " " + str(X[i]) + "," + str(Y[i])
return d
def filter_waves(self, waves):
i = 0
while i < len(waves) - 1:
if i > 0: # check if wave is smaller than the last and should be removed
a_pos, a_ht, a_sd = waves[i - 1]
b_pos, b_ht, _b_sd = waves[i]
if b_ht < a_ht and b_pos < a_pos + 3 * a_sd:
waves.pop(i)
continue
if i < len(waves) - 2: # check if wave is smaller than the next and should be removed
a_pos, a_ht, _a_sd = waves[i]
b_pos, b_ht, b_sd = waves[i + 1]
if a_ht < b_ht and a_pos < b_pos - 3 * b_sd:
waves.pop(i)
continue
i += 1
return waves
def make_trace_chipseq(self, waves): # pos, height, stddev, horizontal = True, y_median = 0, sigmas = 3):
''' path points will be at (-3stddev,0), (0,height), (3stddev,0)
Control points at (-1stddev,0), (-1stddev,height), (1stddev,height), (1stddev,0)
'''
waves = sorted(waves)
waves = self.filter_waves(waves)
X = [round((pos - self.start) * self.scale_x, 2) + self.MARGIN for (pos, _height, _stddev) in waves]
# Scale Y and inverse the coordinates
Y = [round(height * self.scale_y, 2) for (_pos, height, _stddev) in waves]
Y = [(self.height - self.BOTTOM_MARGIN - y2) for y2 in Y]
S = [round(stddev * self.scale_x, 2) for (_pos, _height, stddev) in waves]
if (X[0] > S[0]):
d = "M " + str(X[0] - (2 * S[0])) + "," + self.y_bottom + " C" # point 1
d += " " + str(X[0] - (S[0])) + "," + self.y_bottom # control point 1
d += " " + str(X[0] - (S[0])) + "," + str(Y[0]) # control point 2
d += " " + str(X[0]) + "," + str(Y[0]) # actual coordinate
else:
d = "M " + str(X[0]) + "," + str(Y[0]) + " C" # point 1
for i in range(1, len(X)):
if ((3 * S[i]) + (3 * S[i - 1])) < (X[i] - X[i - 1]):
d += " " + str(X[i - 1] + S[i - 1]) + "," + str(Y[i - 1]) # control point 1
d += " " + str(X[i - 1] + 2 * S[i - 1]) + "," + self.y_bottom # control point 2
d += " " + str(X[i - 1] + 3 * S[i - 1]) + "," + self.y_bottom # actual coordinate
d += " " + str(X[i] - S[i]) + "," + self.y_bottom # control point 2
d += " " + str(X[i] - 2 * S[i]) + "," + self.y_bottom # control point 1
d += " " + str(X[i] - 3 * S[i]) + "," + self.y_bottom # actual coordinate
d += " " + str(X[i] - (S[i])) + "," + self.y_bottom # control point 1
d += " " + str(X[i] - (S[i])) + "," + str(Y[i]) # control point 2
d += " " + str(X[i]) + "," + str(Y[i]) # actual coordinate
else:
d += " " + str(X[i - 1] + round((X[i] - X[i - 1]) / 4, 2)) + "," + str(Y[i - 1]) # control point 1
d += " " + str(X[i] - round((X[i] - X[i - 1]) / 4, 2)) + "," + str(Y[i]) # control point 2
d += " " + str(X[i]) + "," + str(Y[i]) # actual coordinate
last = len(X) - 1
d += " " + str(X[last] + (S[last])) + "," + str(Y[last]) # control point 1
d += " " + str(X[last] + (S[last])) + "," + self.y_bottom # control point 2
d += " " + str(X[last] + (2 * S[last])) + "," + self.y_bottom # actual coordinate
return d
def make_trace_meth(self, data): # pos, height, stddev, horizontal = True, y_median = 0, sigmas = 3):
''' path points will be at (-3stddev,0), (0,height), (3stddev,0)
Control points at (-1stddev,0), (-1stddev,height), (1stddev,height), (1stddev,0)
'''
data = sorted(data)
X = [round((pos - self.start) * self.scale_x, 2) + self.MARGIN for (pos, _mean) in data]
# Scale Y and inverse the coordinates
Y = [mean for (_pos, mean) in data]
d = "M " + str(X[0]) + "," + str(Y[0]) + " C" # point 1
for i in range(1, len(X)):
d += " " + str(X[i - 1] + round((X[i] - X[i - 1]) / 4, 2)) + "," + str(Y[i - 1]) # control point 1
d += " " + str(X[i] - round((X[i] - X[i - 1]) / 4, 2)) + "," + str(Y[i]) # control point 2
d += " " + str(X[i]) + "," + str(Y[i]) # actual coordinate
return d
def build_chipseq(self, message, waves, trace):
'''convert loaded data into svg images'''
if message:
Message = Text('[ ' + message + ' ]', insert = (float(self.width) / 3.0, float(self.height) / 2.0),
fill = "black", font_size = bigfont * 2)
self.elements.append(Message)
heights = [] # create path objects for each peak
if not waves:
return
for (pos, height, stddev, sample_id) in waves:
heights.append(height)
self.maxh = max(heights)
self.scale_y = self.dimension_y / self.maxh
samples = {}
if trace:
for (pos, height, stddev, sample_id) in waves:
if sample_id in samples:
samples[sample_id].append((pos, height, stddev))
else:
samples[sample_id] = []
samples[sample_id].append((pos, height, stddev))
for sampleid in samples:
w = samples[sampleid]
d = self.make_trace_chipseq(w)
types_color, _new = self.palette.colour_assignment_group(sampleid)
self.elements.append(Path(stroke = types_color, stroke_width = 2,
stroke_linecap = 'round', stroke_opacity = 0.8, d = d, fill = 'none',
onmouseover = "evt.target.ownerDocument.getElementById('sample_name').firstChild.data = \'%s\'" %
(''.join(s for s in sampleid if s in string.printable))))
else:
for (pos, height, stddev, sample_id) in waves:
d = self.make_gausian(pos, height, stddev)
types_color, _new = self.palette.colour_assignment_group(sample_id)
self.elements.append(Path(stroke = types_color, stroke_width = 0.1,
stroke_linecap = 'round', stroke_opacity = 0.8,
fill = types_color, fill_opacity = 0.5, d = d,
onmouseover = "evt.target.ownerDocument.getElementById('sample_name').firstChild.data = \'%s\'" %
(''.join(s for s in sample_id if s in string.printable))))
# fix to truncate curves at border (to hide them)
self.elements.append(Rect(insert = (0, self.BOTTOM_MARGIN), size = (self.MARGIN + 1, self.height - self.MARGIN), stroke = types_color, stroke_width = 0.0, fill = "#ffffff", fill_opacity = 1))
self.elements.append(Rect(insert = (self.width - self.RIGHT_MARGIN, 0), size = (self.RIGHT_MARGIN, self.height - self.MARGIN), stroke = types_color, stroke_width = 0.0, fill = "#ffffff", fill_opacity = 1))
self.palette.purge_unused()
def build_methylation(self, message, pos_betas_dict, sample_peaks, show_points, show_peaks, show_groups, probes_by_pos, probe_details, bigger_dists, trace):
'''convert this information into elements of the svg image'''
self.scale_y = 1
ht = 0
if bigger_dists:
ht = self.METHYLATION_DISTR_HT_BIG
else:
ht = self.METHYLATION_DISTR_HT_MED
if message:
Message = Text('[ ' + message + ' ]', insert = (float(self.width) / 3.0, float(self.height) / 2.0),
fill = "black", font_size = bigfont * 2)
self.elements.append(Message)
samples = {}
for position in pos_betas_dict.keys():
x = round(float(position - self.start) * self.scale_x, 2) + self.MARGIN
probeid = probes_by_pos[position]
if show_points:
for beta, sample_id, sample_type in pos_betas_dict[position]:
sample_id = str(sample_id)
sample_type = str(sample_type)
y = round((1 - beta) * self.dimension_y, 2) + self.MARGIN
type_color, sample_color, new = self.palette.colour_assignment(sample_type, sample_id)
if new:
show_groups.append(sample_type)
if not show_groups or sample_type in show_groups:
point = Circle(center = (x, y), r = self.METHYLATION_DOT_RADIUS, fill = sample_color,
onmouseover = "evt.target.ownerDocument.getElementById('sample_name').firstChild.data = \'%s %s-%s \'" %
(probeid, sample_type, sample_id))
self.elements.append(point)
if show_peaks or trace:
for sample_type in sample_peaks[position]:
if not show_groups or sample_type in show_groups:
if self.gausian_colour.has_key(sample_type):
type_color = self.gausian_colour[sample_type]
else:
type_color, new = self.palette.colour_assignment_group(sample_type)
self.gausian_colour[sample_type] = type_color
m, s = sample_peaks[position][sample_type]
m = round((1 - m) * self.dimension_y, 2) + self.MARGIN
s = round(s * self.dimension_y, 3)
if trace:
if sample_type in samples:
samples[sample_type].append((position, m))
else:
samples[sample_type] = []
samples[sample_type].append((position, m))
if show_peaks and s != 0.0:
d = self.make_gausian(position, ht, s, False, m)
gaussian = (Path(stroke = type_color,
stroke_width = self.DISTR_STROKE,
stroke_linecap = 'round',
stroke_opacity = 0.8,
fill = type_color,
fill_opacity = 0.1,
d = d))
self.elements.insert(1, gaussian)
if trace:
for sample_type in samples:
if self.gausian_colour.has_key(sample_type):
type_color = self.gausian_colour[sample_type]
else:
type_color, new = self.palette.colour_assignment_group(sample_type)
self.gausian_colour[sample_type] = type_color
d = self.make_trace_meth(samples[sample_type])
t = (Path(stroke = type_color,
stroke_width = 2,
stroke_linecap = 'round',
stroke_opacity = 0.8,
fill = "none",
onmouseover = "evt.target.ownerDocument.getElementById('sample_name').firstChild.data = \'%s\'" % (sample_type) ,
d = d))
self.elements.insert(1, t)
# fix to truncate curves at border (to hide them)
if show_peaks:
self.elements.append(Rect(insert = (0, 0), size = (self.width, self.MARGIN), stroke_width = 0, fill = "#ffffff", fill_opacity = 1))
self.elements.append(Rect(insert = (0, self.height - self.BOTTOM_MARGIN), size = (self.width, self.dimension_x - self.height), stroke_width = 0, fill = "#ffffff", fill_opacity = 1))
for position in pos_betas_dict.keys():
probeid = probes_by_pos[position]
x = round(float(position - self.start) * self.scale_x, 2) + self.MARGIN
if probe_details[probeid]['n_snpcpg'] > 0: # must process this after the rect, which would cover them otherwise
point = Rect(insert = (x - 1.0, self.MARGIN + self.dimension_y), size = (2.0, 8.0), stroke_width = 0, fill = 'red',
onmouseover = "evt.target.ownerDocument.getElementById('sample_name').firstChild.data = \'SNP in cpg: %s\'" %
(probeid))
self.elements.append(point)
elif probe_details[probeid]['n_snpprobe'] > 0:
point = Rect(insert = (x - 1.0, self.MARGIN + self.dimension_y), size = (2.0, 8.0), stroke_width = 0, fill = 'blue',
onmouseover = "evt.target.ownerDocument.getElementById('sample_name').firstChild.data = \'SNP in probe %s\'" %
(probeid))
self.elements.append(point)
self.palette.purge_unused()
def save(self):
''' push loaded elements to the the plot, clear out the elements. '''
for element in self.elements:
self.plot.add(element)
self.elements = None # may want to remove this, if we ever want to do fancy stuff with the elements.
self.plot.save()
def to_string(self):
''' convert the loaded elements to strings and return the list of elements'''
magic_box = Text(" ", id = "sample_name", insert = ((self.MARGIN + 20), (self.MARGIN + 20)),
fill = "black", font_size = medfont)
self.elements.append(magic_box)
t0 = time.time()
temp = []
temp.append(self.plot.tostring().replace("</svg>", ""))
for element in self.elements:
temp.append(element.tostring())
temp.append("</svg>")
print " Conversion of SVG to string took %f seconds" % (time.time() - t0)
return ''.join(t for t in temp)
def get_elements(self):
''' call sample labels and delete loaded elements. '''
self.add_sample_labels(self.MARGIN * 3.2 + self.width)
return self.elements
def get_xml(self):
''' Convert the loaded elements into XML strings and then return them.'''
strings = ""
for element in self.elements:
strings += (element.get_xml().decode('utf-8'))
return strings
def add_legends(self, get_cpg, annotations):
''' Add annotations, title, axis, tic marks and labels '''
Title = Text(self.title, insert = (bigfont + ((float(self.MARGIN) - bigfont) / 3),
bigfont + ((float(self.MARGIN) - bigfont) / 3)),
fill = legend_color, font_size = bigfont)
self.elements.append(Title)
for axis in get_axis(self.width, self.MARGIN, self.height, self.BOTTOM_MARGIN, self.RIGHT_MARGIN):
self.elements.append(axis)
# print "add_legends, messages are: %s" % self.message
if self.message is None:
self.add_xtics()
# self.add_sample_labels(self.width - self.RIGHT_MARGIN + 20)
if get_cpg:
for cpg in add_cpg(annotations, self.MARGIN, self.height, self.scale_x, self.start, self.end, self.BOTTOM_MARGIN):
self.elements.insert(0, cpg)
def add_xtics(self):
''' Create X tics on the plot'''
scale_tics = 1
while((scale_tics * 10) < self.end - self.start):
scale_tics *= 10
xtics = [i for i in range(self.start, self.end + 1) if i % (scale_tics) == 0]
while len(xtics) < 4:
scale_tics /= 2
xtics += [j for j in range(self.start, self.end + 1) if j % (scale_tics) == 0 and j not in xtics]
xtics.sort()
spacing = fabs((self.MARGIN + (xtics[1] - self.start) * self.scale_x) - (self.MARGIN + (xtics[0] - self.start) * self.scale_x)) / 4
for tic in xtics:
tic_x = (self.MARGIN + (tic - self.start) * self.scale_x)
tic_y = self.height - self.BOTTOM_MARGIN + smallfont * 1.5
ticmarker = (Text(str(tic), insert = (tic_x, tic_y), fill = legend_color, font_size = smallfont))
ticline = Rect(insert = (tic_x, self.height - self.BOTTOM_MARGIN - 2), size = (1, 5), fill = legend_color)
for i in range (1, 4):
if tic_x - spacing * i > self.MARGIN - 5:
ticline2 = Rect(insert = (tic_x - spacing * i, self.height - self.BOTTOM_MARGIN - 2), size = (1, 2), fill = legend_color)
self.elements.append(ticline2)
self.elements.append(ticline)
self.elements.append(ticmarker)
def add_ytics_chipseq(self):
''' Add Y ticks to the svg plot '''
if self.maxh: steps = round(self.maxh / 5, 1)
labels = [0, steps, 2 * steps, 3 * steps, 4 * steps, 5 * steps]
ytics = [round(self.height - self.BOTTOM_MARGIN - (self.dimension_y / 5 * y), 3) for y in range(0, 6)]
spacing = (ytics[0] - ytics[1]) / 2
for tic, label in zip(ytics, labels):
ticline = Rect(insert = (self.MARGIN - 2, tic), size = (5, 1), fill = legend_color)
if tic - spacing > self.MARGIN:
ticline2 = Rect(insert = (self.MARGIN - 2, tic - spacing), size = (2, 1), fill = legend_color)
self.elements.append(ticline2)
tic_x = self.MARGIN - smallfont * 2
tic_y = tic + 1
if len(str(label)) == 1:
tic_x += 3
if len(str(label)) == 2:
tic_x += 2
if len(str(label)) >= 3:
tic_x -= 10
ticmarker = (Text(label, insert = (tic_x, tic_y), fill = legend_color, font_size = smallfont))
self.elements.append(ticline)
self.elements.append(ticmarker)
def add_ytics_methylation(self):
''' Add Y ticks to the svg plot '''
labels = [0, 0.2, 0.4, 0.6, 0.8, 1]
ytics = [round((self.MARGIN + self.dimension_y) - (y * self.dimension_y), 3) for y in labels]
spacing = (ytics[0] - ytics[1]) / 2
for tic, label in zip(ytics, labels):
ticline = Rect(insert = (self.width - self.RIGHT_MARGIN, tic), size = (5, 1), fill = legend_color)
if tic - spacing > self.MARGIN:
ticline2 = Rect(insert = (self.width - self.RIGHT_MARGIN, tic - spacing), size = (2, 1), fill = legend_color)
self.elements.append(ticline2)
tic_x = self.width - self.RIGHT_MARGIN + smallfont
tic_y = tic + 1
if len(str(label)) == 1:
tic_x += 3
if len(str(label)) == 2:
tic_x += 2
ticmarker = (Text(label, insert = (tic_x, tic_y), fill = legend_color, font_size = smallfont))
self.elements.append(ticline)
self.elements.append(ticmarker)
def draw_genes(self, genes):
for gene in genes:
for transcript in gene['transcripts']:
start = self.convert_xcoord_to_pos(gene['start'])
length = self.convert_xcoord_to_pos(gene['end']) - start
if start < self.MARGIN:
if start < 0: # first, remove anything before zero.
length += start
start = 0
length -= (self.MARGIN + start) # then remove anything before the margin begins
start = self.MARGIN
if start + length > (self.width - self.RIGHT_MARGIN):
length = (self.width - self.RIGHT_MARGIN) - start
text = None
if gene['strand'] == 1:
text = gene['name'] + " ->>>"
else:
text = " <<<- " + gene['name']
# print "(self.width + self.RIGHT_MARGIN + self.MARGIN)", (self.width - self.RIGHT_MARGIN)
# print "gene -> text:%s chrend:%i chrstart:%i start:%i length:%i" % (gene['name'], gene['end'], gene['start'], start, length)
g = Rect(insert = (start, self.height - self.BOTTOM_MARGIN + self.gene_offset + 4), size = (length, 2), fill = "grey")
t = (Text(text, insert = (start, self.height - self.BOTTOM_MARGIN + self.gene_offset + 9), fill = legend_color, font_size = smallfont))
self.elements.append(g)
for exon in gene["transcripts"][transcript]["exons"]:
e = gene["transcripts"][transcript]["exons"][exon]
e_start = self.convert_xcoord_to_pos(e["start"])
e_len = self.convert_xcoord_to_pos(e['end']) - e_start
if e_start > (self.width - self.RIGHT_MARGIN) or (e_start + e_len) < self.MARGIN:
continue
if e_start < self.MARGIN:
e_start = self.MARGIN
if e_start + e_len > (self.width - self.RIGHT_MARGIN):
e_len = (self.width - self.RIGHT_MARGIN) - e_start
e = Rect(insert = (e_start, self.height - self.BOTTOM_MARGIN + self.gene_offset), size = (e_len, 9), fill = "grey")
self.elements.append(e)
self.elements.append(t)
self.gene_offset += 12
if self.gene_offset > 250:
self.gene_offset = self.GENE_OFFSET