def _create_lines(self):
for row in self.line_rows:
# Create an object to construct the necessary components
forest_obj = ForestLine(row, self.coefficient_radius, self.rounder,
self.text_colour)
if forest_obj.var_name == "#Delete":
self.height_max -= self.height_iter
else:
self.bound_values = self.bound_values + [
float(forest_obj.lb),
float(forest_obj.ub)
]
# Create the line
current_name = forest_obj.make_line(self.height_max,
self.height_iter,
self.y_scale)
y_mean = forest_obj.make_coefficient(current_name)
# Set the variable name
make_text(f"{forest_obj.var_name}_var_name", -self.var_bound,
y_mean, forest_obj.var_name, self.height_iter,
self.text_colour, "LEFT")
# Create the numeric string
numeric = f"{set_values(forest_obj.coef, self.rounder)} ({set_values(forest_obj.lb, self.rounder)}; " \
f"{set_values(forest_obj.ub, self.rounder)})"
make_text(f"{forest_obj.var_name}_CI", 1 + self.ci_bound,
y_mean, numeric, self.height_iter, self.text_colour)
self.height_max -= self.height_iter
def make_group(self, group, points):
print(group)
obj, x_mid = self.make_vertex_holder(group, points)
if x_mid != 0:
make_text(group, x_mid, -(self._text_scale + 1), group,
self._text_scale, self._text_colour, 'CENTER')
self.link_ico(obj)
def _make_text_and_box(self, name, col_i, position, previous_height):
# Set the width, which is the x position, relative to other columns of this row
width = sum([self.widths[str(i - 1)] for i in range(col_i + 1)])
if col_i != 0:
width += self.spacing
# Create the text object and set its origin to geometry
obj = make_text(name, width, previous_height, position["Text"], 1, self.text_colour,
align="CENTER")
obj.select_set(True)
bpy.ops.object.origin_set(type='ORIGIN_GEOMETRY', center='MEDIAN')
# Isolate the texts center from location and width and height from dimensions
x, y, _ = obj.location / 2
x_d, y_d, _ = obj.dimensions / 2
obj.select_set(False)
self._make_bounding_box(x, y, x_d, y_d, name, obj)
def _set_dimensions(self):
widths = {"-1": 0}
dimension_dict = {}
for i in range(self.col_count):
dimensions = []
for name, position in self.positions.items():
col_id, row_id = name.split("-")
if col_id == str(i):
obj = make_text(name, 0, 0, position["Text"], 1, self.text_colour, align="CENTER")
dimensions.append(obj.dimensions)
x, y, z = obj.dimensions
dimension_dict[name] = [x, y, z]
widths[str(i)] = max([x for x, y, z in dimensions])
collection_cleanup("Collection")
return widths, dimension_dict
def _make_axis(self, x_axis_width, axis_colour, line_density, axis_width, bound, significance, significance_colour):
# Set the axis y height as the max of axis_y_positions with ceiling to prevent out of bounds points
axis_height = math.ceil(max(self.axis_y_positions))
# Make the graphs axis
make_graph_axis(axis_colour, x_axis_width, axis_height, axis_width, bound)
# make the horizontal dashed line to determine the level of significance
make_horizontal_dashed_line("Line", significance_colour, x_axis_width, 0, significance, line_density)
# Make a spacer so that elements are relative distances to the axis
axis_spacer = -(axis_width + (axis_width * 2) + axis_width / 2)
# Label the x axis
make_text("Chromosomes", 23.5 / 2, axis_spacer*1.5, "Chromosomes", axis_width * 2, axis_colour, "CENTER")
for i in range(23):
make_text(f"Chr{i}", i + 0.5, axis_spacer, f"{i + 1}", axis_width * 2, axis_colour, "CENTER")
# Label the y axis
make_text("Log", axis_spacer * 1.5, axis_height / 2, "-log10(pvalue)", axis_width * 2, axis_colour, "CENTER")
# Y axis needs to be rotated
obj = bpy.data.objects["Log"]
obj.select_set(True)
bpy.ops.transform.rotate(value=1.5708, orient_axis='Z', orient_type='GLOBAL',
orient_matrix=((1, 0, 0), (0, 1, 0), (0, 0, 1)), orient_matrix_type='GLOBAL',
constraint_axis=(False, False, True), mirror=True, use_proportional_edit=False,
proportional_edit_falloff='SMOOTH', proportional_size=1,
use_proportional_connected=False, use_proportional_projected=False)
# Add y axis values
for i in range(axis_height + 1):
if i % 2 == 0:
make_text(f"log{i}", axis_spacer, i, f"{i}", axis_width * 2, axis_colour, "CENTER")
# Render the scene
render_scene(self.camera_position, self.write_directory, f"{self.write_name}__AXIS", x_resolution=self.x_res,
y_resolution=self.y_res, camera_scale=self.camera_scale)
def _create_axis(self):
# Make y axis from the min and max values of the standardised rows
self._make_axis()
self.height_max -= self.height_iter
# Label left an right most columns
make_text("Phenotype", -self.var_bound, self.height_iter, "Phenotype",
self.height_iter, self.text_colour)
make_text(self.value_title, 1 + self.ci_bound, self.height_iter,
self.value_title, self.height_iter, self.text_colour)
# Add values based on a range between the min and max equally divided
make_text("Min_Bound", 0, self.height_max,
set_values(min(self.bound_values), 2), self.height_iter,
self.text_colour)
make_text("Max_Bound", 1, self.height_max,
str(round(max(self.bound_values), 2)), self.height_iter,
self.text_colour, "RIGHT")
make_text("Mid_Point", self.axis_position, self.height_max,
str(self.axis_target), self.height_iter, self.text_colour,
"CENTER")
# # Add the x axis label
make_text("Axis Label",
self.axis_position,
self.height_max - self.height_iter,
self.axis_label,
self.height_iter,
self.text_colour,
align="CENTER")
def make_y_axis(self):
iterator = math.ceil(max(self._y_max)) / 10
for i in range(1, 11):
make_text(str(iterator * i), -(self._text_scale + 1), iterator * i,
str(round(iterator * i, 2)), self._text_scale,
self._text_colour, 'RIGHT')
def label_points(self, points, x_points, i, y):
name = points[i][self.name_index]
make_text(name, x_points[i] + (2 * self.ico_scale), y, name,
self._label_scale, self._text_colour)
def _axis(self, x_values, y_values, set_bounds, line_width, axis_colour):
# Make the 45% line from the min of the max
end_point = min([max(y_values), max(x_values)])
line, line_mesh = make_mesh("Line", axis_colour)
line_mesh.from_pydata([(0, 0, 0), (end_point, end_point, 0)], [(0, 1)],
[])
# Turn line to curve, add width equal to line_width
line.select_set(True)
bpy.ops.object.convert(target='CURVE')
bpy.context.object.data.bevel_resolution = 0
bpy.context.object.data.bevel_depth = line_width
# Create the bounds
x_bound = max(x_values)
y_bound = max(y_values)
# define the Bound of the axis
if set_bounds != "None":
x, y = tuple_convert(set_bounds)
if (x_bound > x) or (y_bound > y):
x = max([x_bound, x])
y = max([y_bound, y])
self.logger.write(
F"WARNING: Set Bound is smaller than p value's, defaulting to native bound"
)
else:
x, y = x_bound, y_bound
# Make the graphs axis
make_graph_axis(axis_colour, x, y, line_width, 0.0)
# TODO see if we can generalise the axis for make graph axis to also include the annotation
# Label the x axis
make_text("Theoretical -log10",
math.floor(x) / 2, -1, "Theoretical -log10", 0.5,
axis_colour, "CENTER")
for i in range(math.floor(x)):
make_text(f"{i}", i + 0.5, -0.5, f"{i + 1}", 0.5, axis_colour,
"CENTER")
# Label the y axis
make_text("Observed -log 10", -1,
math.floor(y) / 2, "Observed -log 10", 0.5, axis_colour,
"CENTER")
# Y axis needs to be rotated
obj = bpy.data.objects["Observed -log 10"]
obj.select_set(True)
bpy.ops.transform.rotate(value=1.5708,
orient_axis='Z',
orient_type='GLOBAL',
orient_matrix=((1, 0, 0), (0, 1, 0), (0, 0,
1)),
orient_matrix_type='GLOBAL',
constraint_axis=(False, False, True),
mirror=True,
use_proportional_edit=False,
proportional_edit_falloff='SMOOTH',
proportional_size=1,
use_proportional_connected=False,
use_proportional_projected=False)
for i in range(math.floor(y)):
make_text(f"log{i}", -0.5, i + 0.5, f"{i + 1}", 0.5, axis_colour,
"CENTER")
# Render the scene
render_scene(self.camera_position,
self.write_directory,
f"{self.write_name}__AXIS.png",
"BLENDER_EEVEE",
self.x_res,
self.y_res,
camera_scale=self.camera_scale)
self.logger.write(f"Written the AXIS out at {terminal_time()}")
def make_name(self, i, row):
"""Make the x axis text"""
make_text(row[self.name_i], i + 0.5, -1, row[self.name_i], 1, (0, 0, 0, 1), align='CENTER')