def make_map_with_donuts(counts, outprefix, europe=False, debug=False):
donut_coords = {
'Australia': (369, 193),
'Belgium': (195, 123),
'Canada': (88, 91),
'China': (330, 123),
'Germany': (255, 120),
'Italy': (285, 207),
'Netherlands': (210, 105),
'Pakistan': (288, 132),
'Peru': (115, 180),
'Russia': (314, 91),
'Serbia': (372, 194),
'Sierra Leone': (190, 150),
'South Africa': (233, 201),
'Spain': (110, 230),
'Swaziland': (258, 210),
'Thailand': (328, 143),
'UK': (131, 96),
'Uzbekistan': (282, 114),
'Europe': (210, 110),
}
no_donuts_svg = f'{outprefix}.tmp.svg'
final_svg = f'{outprefix}.svg'
final_pdf = final_svg.replace('.svg', '.pdf')
donut_files = make_donuts(counts, outprefix)
make_map_no_donuts(no_donuts_svg, europe=europe)
donut_size = 40 if europe else 32
with open(no_donuts_svg) as f:
svg_lines = [x.rstrip() for x in f]
assert svg_lines[-1] == '</svg>'
last_svg_line = svg_lines.pop()
# line to point to Swaziland
if not europe:
svg_lines.append(
'<line x1="280" y1="230" x2="262" y2="212" style="stroke:rgb(0,0,0);stroke-width:1" />'
)
for country in donut_files:
x, y = donut_coords[country]
filename = os.path.abspath(donut_files[country])
svg_lines.append(
f'<image x="{x}" y="{y}" width="{donut_size}" height="{donut_size}" xlink:href="file:{filename}"></image>'
)
svg_lines.append(last_svg_line)
with open(final_svg, 'w') as f:
print(*svg_lines, sep='\n', file=f)
svg.svg2pdf(final_svg, final_pdf)
if not debug:
os.unlink(no_donuts_svg)
os.unlink(final_svg)
for filename in donut_files.values():
os.unlink(filename)
def make_legend(outprefix, debug=False):
svg_file = f'{outprefix}.svg'
pdf_file = f'{outprefix}.pdf'
s = r''' <svg height="70pt" width="70pt">
<text x="10" y="11">Dataset</text>
<circle cx="11" cy="30" r="10" stroke="black" stroke-width="0.5" fill="''' + mykrobe_colour + r'''" />
<text x="23" y="35">Training</text>
<circle cx="11" cy="55" r="10" stroke="black" stroke-width="0.5" fill="''' + validate_colour + r'''" />
<text x="23" y="60">Validation</text>
<circle cx="11" cy="80" r="10" stroke="black" stroke-width="0.5" fill="''' + test_colour + r'''" />
<text x="23" y="85">Test</text>
</svg>'''
with open(svg_file, 'w') as f:
print(textwrap.dedent(s), file=f)
svg.svg2pdf(svg_file, pdf_file)
if not debug:
os.unlink(svg_file)
def make_legend(tools, outfile, header=None):
font_size = 14
square_len = 20
y_space = 3
svg_lines = []
y = 10
square_left = 5
square_right = square_left + square_len
total_width = 200
if header is not None:
svg_lines.append(
svg.svg_text(square_right,
y,
header,
font_size + 1,
position='start',
vertical_align='middle'))
y += 15
for tool in tools:
svg_lines.append(
svg.svg_rectangle(square_left, y, square_right, y + square_len,
common_data.tool_colours[tool], 'black'))
svg_lines.append(
svg.svg_text(square_right + 5,
y + 0.5 * square_len,
common_data.tool_names[tool],
font_size,
position='start',
vertical_align='middle'))
y += square_len + y_space
f = open(outfile, 'w')
print(r'''<?xml version="1.0" standalone="no"?>
<!DOCTYPE svg PUBLIC " -//W3C//DTD SVG 1.0//EN" "http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd">
<svg width="''' + str(total_width) + '" height="' + str(y) + '">',
file=f)
print(*svg_lines, sep='\n', file=f)
print('</svg>', file=f)
f.close()
svg.svg2pdf(outfile, outfile.replace('.svg', '.pdf'))
def plot_one_tool(data, outfile, ignore=None, y_scale=0.8):
assert outfile.endswith('.svg')
to_ignore = {}
if ignore is not None:
data = copy.deepcopy(data)
for k1, k2 in ignore:
if k1 in data and k2 in data[k1]:
if k1 not in to_ignore:
to_ignore[k1] = {}
to_ignore[k1][k2] = data[k1][k2]
del data[k1][k2]
if len(data[k1]) == 1:
del data[k1]
for k in data:
try:
del data[k][99]
except:
pass
colours = [
'#f0e8e3',
'#e2d3c9',
'#f5cfb6',
'#FDD49E',
'#FDBB84',
'#FCA964',
'#FC8D59',
'#E34A33',
'#d81529',
'#CE1256',
'#980043',
'#400013'
]
truth_nodes = {}
called_nodes = {}
edges = []
for truth in data:
if truth not in truth_nodes:
truth_nodes[truth] = {}
for called in data[truth]:
if called not in called_nodes:
called_nodes[called] = {}
truth_nodes[truth][called] = data[truth][called]
called_nodes[called][truth] = data[truth][called]
edges.append((truth, called, data[truth][called]))
plot_width = 1050
drugs = OrderedDict([
('H', 'Isoniazid'),
('R', 'Rifampicin'),
('Z', 'Pyrazinamide'),
('E', 'Ethambutol'),
('Rfb', 'Rifabutin'),
('Rpt', 'Rifapentine'),
('Lfx', 'Levofloxacin'),
('Mfx', 'Moxifloxacin'),
('Gfx', 'Gatifloxacin'),
('S', 'Streptomycin'),
('Km', 'Kanamycin'),
('Am', 'Amikacin'),
('Cm', 'Capreomycin'),
('PAS', 'Para-aminosalicylate/Para-aminosalicylate-sodium'),
('Eto', 'Ethionamide'),
('Pto', 'Prothionamide'),
('Cs', 'Cycloserine'),
('Trd', 'Terizidone'),
('Cfz', 'Clofazimide'),
('Lzd', 'Linezolid'),
('hH', 'High dose Isoniazid'),
('hZ', 'High dose Pyrazinamide'),
('hE', 'High dose Ethambutol'),
('X', 'Amox-Clavulanate, Imipenem/Cilastatin, Meropenem, High dose Isoniazid (if possible)'),
])
regimen_to_drug = {
1: {'req': ('H', 'R', 'Z', 'E')},
2: {'req': ('R', 'Z', 'E'), 'opt': ((1, 'Lfx', 'Mfx', 'Gfx'),)},
3: {'req': ('R', 'Z', 'E')},
4: {'req': ('R', 'E', (1, 'Lfx', 'Mfx', 'Gfx'))},
5: {'req': ('R', 'Z', (1, 'Lfx', 'Mfx', 'Gfx'))},
6: {'req': ('R', 'E', (1, 'Lfx', 'Mfx', 'Gfx'), (1, 'Km', 'Am', 'Cm'), (1, 'Eto', 'Pto', 'PAS', 'Cs', 'Trd'))},
7: {'req': ('R', 'E', 'S', (1, 'Eto', 'Pto', 'PAS', 'Cs', 'Trd'))},
8: {'req': ('H', 'R', 'E')},
9: {'req': ('H', 'R', 'Z')},
10: {'req': ('Z', (1, 'Lfx', 'Mfx', 'Gfx'), (1, 'Km', 'Am', 'Cm'), (2, 'Eto', 'Pto', 'Cs', 'Trd', 'Cfz', 'Lzd')), 'opt': ('hH', 'hE')},
11: {'req': ((1, 'Gfx', 'Mfx'), 'Km', 'Pto', 'Cfz', 'hH', 'hE', 'hZ', )},
12: {'req': ('Rfb', 'Rpt', 'E', 'Z', (1, 'Lfx', 'Mfx', 'Gfx'), (1, 'Km', 'Am', 'Cm', 'S'), 'Eto', 'Pto', 'PAS', 'Cs', 'Trd', 'hH', 'X')},
}
regimen_to_pheno = {
1: {'H': 'S', 'R': 'S', 'Z': 'S', 'E': 'S'},
2: {'H': 'R', 'R': 'S', 'Z': 'S', 'E': 'S'},
3: {'H': 'R', 'R': 'S', 'Z': 'S', 'E': 'S', 'Mfx': 'R'},
4: {'H': 'R', 'R': 'S', 'Z': 'R', 'E': 'S'},
5: {'H': 'R', 'R': 'S', 'Z': 'S', 'E': 'R'},
6: {'H': 'R', 'R': 'S', 'Z': 'R', 'E': 'R'},
7: {'H': 'R', 'R': 'S', 'Z': 'R', 'E': 'R', 'Km': 'R', 'Am': 'R', 'Cm': 'R', 'S': 'S'},
8: {'H': 'S', 'R': 'S', 'Z': 'R', 'E': 'S'},
9: {'H': 'S', 'R': 'S', 'Z': 'S', 'E': 'R'},
10: {'H': '(R)', 'R': 'R'},
11: {'H': '(R)', 'R': 'R', 'Km': 'S', 'Mfx': 'S'},
12: {'H': 'R', 'R': 'R', 'Mfx': 'R'},
}
drug_col_width = 26
svg_lines = []
x = 10
headings_y = 20
drug_to_x_centre = {}
for drug in drugs:
drug_to_x_centre[drug] = x + 0.5 * drug_col_width
svg_lines.append(svg.svg_text(x + 0.5 * drug_col_width, headings_y, drug, 12, vertical_align='middle'))
x += drug_col_width
x += 80
right_half_x_left = x + 10
node_to_edge_space = 50
left_node_x = right_half_x_left + node_to_edge_space
node_width = 20
right_node_x = plot_width - node_to_edge_space - node_width
y_start = 40
node_y_gap = 30
svg_node_lines = []
truth_nodes_y_tops = {}
truth_nodes_y_bottoms = {}
called_nodes_y_tops = {}
truth_node_to_y_centre = {}
# Nodes on the left
y = y_start
svg_lines.append(svg.svg_text(left_node_x - 110, headings_y, 'Regimen', 11, position='middle', font_family='arial', vertical_align='middle'))
svg_lines.append(svg.svg_text(left_node_x - 5, headings_y, 'Samples', 11, position='end', font_family='arial', vertical_align='middle'))
for node in regimen_to_drug:
if node-1 not in truth_nodes:
truth_nodes[node-1] = {}
if node-1 not in called_nodes:
called_nodes[node-1] = {}
for node, node_counts in sorted(truth_nodes.items()):
truth_nodes_y_tops[node] = y
if len(node_counts) > 0:
total_samples = sum(node_counts.values())
else:
total_samples = 0
node_y_bottom = y + y_scale * total_samples
truth_node_to_y_centre[node] = 0.5 * (y + node_y_bottom)
svg_node_lines.append(svg.svg_rectangle(left_node_x, y, left_node_x + node_width, node_y_bottom,
colours[int(node)], colours[int(node)], border_width=1))
#svg_lines.append(svg.svg_text(left_node_x - 110, 0.5 * (y + node_y_bottom),
# who_treatment.regimens[node+1].definition, 11, position='start', font_family='arial', vertical_align='middle'))
svg_lines.append(svg.svg_text(left_node_x - 110, 0.5 * (y + node_y_bottom), str(node+1), 11, position='middle', font_family='arial', vertical_align='middle'))
svg_lines.append(svg.svg_text(left_node_x - 5, 0.5 * (y + node_y_bottom),
str(total_samples), 11, position='end', font_family='arial', vertical_align='middle'))
if node in to_ignore:
total_ignored = sum(to_ignore[node].values())
svg_lines.append(svg.svg_text(left_node_x - 5, 0.5 * (y + node_y_bottom) + 12,
f'(+{total_ignored})', 11, position='end', font_family='arial', vertical_align='middle'))
y = node_y_bottom + node_y_gap
truth_nodes_y_bottoms[node] = node_y_bottom
y = y_start
# Nodes on the right
for node, node_counts in sorted(called_nodes.items()):
called_nodes_y_tops[node] = y
total_samples = sum(node_counts.values())
node_y_bottom = y + y_scale * total_samples
svg_node_lines.append(svg.svg_rectangle(right_node_x, y, right_node_x + node_width, node_y_bottom,
colours[int(node)], colours[int(node)], border_width=1))
svg_lines.append(svg.svg_text(right_node_x + node_width + 3, 0.5 * (y + node_y_bottom),
str(total_samples), 11, position='start', font_family='arial', vertical_align='middle'))
if node in to_ignore:
total_ignored = sum(to_ignore[node].values())
svg_lines.append(svg.svg_text(right_node_x + node_width + 3, 0.5 * (y + node_y_bottom) + 12,
f'(+{total_ignored})', 11, position='start', font_family='arial', vertical_align='middle'))
y = node_y_bottom + node_y_gap
# Ribbons
sample_total_counts = {'truth': {}, 'called': {}}
for truth_node, called_node, samples in edges:
if truth_node not in sample_total_counts['truth']:
sample_total_counts['truth'][truth_node] = 0
if called_node not in sample_total_counts['called']:
sample_total_counts['called'][called_node] = 0
y11 = truth_nodes_y_tops[truth_node] + y_scale * sample_total_counts['truth'][truth_node]
sample_total_counts['truth'][truth_node] += samples
y12 = truth_nodes_y_tops[truth_node] + y_scale * sample_total_counts['truth'][truth_node]
y21 = called_nodes_y_tops[called_node] + y_scale * sample_total_counts['called'][called_node]
sample_total_counts['called'][called_node] += samples
y22 = called_nodes_y_tops[called_node] + y_scale * sample_total_counts['called'][called_node]
svg_lines.append(svg.svg_ribbon(left_node_x + node_width, y11, y12, right_node_x, y21, y22,
colours[int(truth_node)], colours[int(truth_node)], border_width=0.5, opacity=0.8))
# Regimen circles and R/S
svg_regimen_lines = []
circle_radius = 0.1 * drug_col_width
y_circle_R_S_offset = 7
pheno_letters_lines = []
for node, regime in regimen_to_drug.items():
y_centre = truth_node_to_y_centre[node-1]
y_circle_centre = y_centre + y_circle_R_S_offset
y_R_or_S = y_centre - y_circle_R_S_offset
for req_or_opt in regime:
if req_or_opt not in regime:
continue
if req_or_opt == 'req':
line_colour = 'black'
else:
line_colour = 'lightgrey'
for drugs_tuple in regime[req_or_opt]:
if type(drugs_tuple) is tuple:
x_min = float('Inf')
x_max = 0
to_append = []
number_of_lines = drugs_tuple[0]
if number_of_lines == 1:
lines_y = [y_circle_centre]
line_width = 1.5
else:
assert number_of_lines == 2
lines_y = [y_circle_centre - circle_radius / 2, y_circle_centre + circle_radius / 2]
line_width = 1
for drug in drugs_tuple[1:]:
to_append.append(svg.svg_circle(drug_to_x_centre[drug], y_circle_centre, 0.2 * drug_col_width, colours[node-1], line_colour, stroke_width=1))
x_min = min(x_min, drug_to_x_centre[drug])
x_max = max(x_max, drug_to_x_centre[drug])
for line_y in lines_y:
svg_regimen_lines.append(svg.svg_line(x_min, line_y, x_max, line_y, line_colour, line_width))
svg_regimen_lines.append(to_append)
else:
svg_regimen_lines.append(svg.svg_circle(drug_to_x_centre[drugs_tuple], y_circle_centre, 0.2 * drug_col_width, colours[node-1], line_colour, stroke_width=1))
for drug, pheno in regimen_to_pheno[node].items():
pheno_letters_lines.append(svg.svg_text(drug_to_x_centre[drug], y_R_or_S, pheno, 10, vertical_align='middle'))
# Make vertical lines to separate drugs
y_top = min(truth_nodes_y_tops.values())
y_top = 5
y_bottom = max(truth_nodes_y_bottoms.values())
y_bottom = y - 5
for drug in drugs:
x_pos = drug_to_x_centre[drug] - 0.5 * drug_col_width
svg_lines.append(svg.svg_line(x_pos, y_top, x_pos, y_bottom, 'lightgrey', 1))
if drug == 'X':
x_pos = drug_to_x_centre[drug] + 0.5 * drug_col_width
svg_lines.append(svg.svg_line(x_pos, y_top, x_pos, y_bottom, 'lightgrey', 1))
# horizontal lines to separate regimens
x_left = min(drug_to_x_centre.values()) - 0.5 * drug_col_width
x_right = left_node_x
y_top_line = truth_nodes_y_tops[0] - 10
svg_lines.append(svg.svg_line(x_left, y_top, x_right, y_top, 'lightgrey', 1))
svg_lines.append(svg.svg_line(x_left, y_top_line, x_right, y_top_line, 'lightgrey', 1))
svg_lines.append(svg.svg_line(x_left, y_bottom, x_right, y_bottom, 'lightgrey', 1))
for i in range(0, len(truth_nodes_y_bottoms) - 1, 1):
y_pos = 0.5 * (truth_nodes_y_bottoms[i] + truth_nodes_y_tops[i+1])
svg_lines.append(svg.svg_line(x_left, y_pos, x_right, y_pos, 'lightgrey', 1))
f = open(outfile, 'w')
print(r'''<?xml version="1.0" standalone="no"?>
<!DOCTYPE svg PUBLIC " -//W3C//DTD SVG 1.0//EN" "http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd">
<svg width="''' + str(plot_width) + '" height="' + str(y) + '">', file=f)
# plot nodes last so that borders are on top of ribbons and therefore still visible
print(*svg_lines, svg_node_lines, svg_regimen_lines, pheno_letters_lines, sep='\n', file=f)
print('</svg>', file=f)
f.close()
svg.svg2pdf(outfile, outfile.replace('.svg', '.pdf'))
def make_plot(stats_dict,
tools,
drugs,
outfile,
first_line=False,
ten_k=False,
how_to_scale='not at all',
susc_gap=None,
susc_xticks=None,
res_xticks=None,
plot_gap_size=30,
extra_width=0):
if susc_gap is not None:
susc_gap_width = susc_gap[1] - susc_gap[0]
stats_dict = copy.deepcopy(stats_dict)
for drug in drugs:
for tool in tools:
if stats_dict[drug][tool]['TN'] > susc_gap[1]:
stats_dict[drug][tool][
'TN'] -= susc_gap_width - plot_gap_size
max_count_res_keys = ['FN', 'TP', 'UNK_R', 'FAIL_R']
max_count_susc_keys = ['FP', 'TN', 'UNK_S', 'FAIL_S']
sample_count = {}
for drug in drugs:
res_counts = set()
susc_counts = set()
for tool in tools:
if tool == '10k_predict':
continue
res_count = sum(
[stats_dict[drug][tool][x] for x in max_count_res_keys])
susc_count = sum(
[stats_dict[drug][tool][x] for x in max_count_susc_keys])
res_counts.add(res_count)
susc_counts.add(susc_count)
assert len(res_counts) == len(susc_counts) == 1
sample_count[drug] = {
'res': res_counts.pop(),
'susc': susc_counts.pop()
}
max_count_res = max([sample_count[x]['res'] for x in sample_count])
max_count_susc = max([sample_count[x]['susc'] for x in sample_count])
centre_space = 20
x_margin = 10
if how_to_scale == 'not at all':
total_width = 600
total_bar_width = total_width - 2 * (centre_space + x_margin)
susc_bar_width = total_bar_width * max_count_susc / (max_count_res +
max_count_susc)
res_bar_width = total_bar_width * max_count_res / (max_count_res +
max_count_susc)
x_centre = x_margin + susc_bar_width + centre_space
elif how_to_scale == 'res susc independent':
total_width = 1000
total_bar_width = total_width - 2 * (centre_space + x_margin)
susc_bar_width = 0.5 * total_bar_width
res_bar_width = 0.5 * total_bar_width
x_centre = total_width / 2
elif how_to_scale == 'all to 100':
total_width = 500
total_bar_width = total_width - 2 * (centre_space + x_margin)
susc_bar_width = 0.5 * total_bar_width - 40
res_bar_width = 0.5 * total_bar_width - 40
x_centre = total_width / 2
bar_height = 13
drug_spacer = 10
x_susc_bar_left = x_centre - centre_space - susc_bar_width
x_res_bar_right = x_centre + centre_space + res_bar_width
y = 20
svg_lines = []
svg_lines.append(
svg.svg_text(0.5 * (x_susc_bar_left + x_centre - centre_space), y,
'Susceptible samples', 20))
svg_lines.append(
svg.svg_text(0.5 * (x_centre + centre_space + x_res_bar_right), y,
'Resistant samples', 20))
y = 45
susc_tick_zeros = len(str(max_count_susc)) - 1
susc_tick_gap = int('1' + '0' * susc_tick_zeros)
susc_ticks = [
-x for x in range(round(-max_count_susc, -susc_tick_zeros), 1,
susc_tick_gap) if x > -max_count_susc
]
res_tick_zeros = len(str(max_count_res)) - 1
res_tick_gap = int('1' + '0' * res_tick_zeros)
res_ticks = list(
range(0,
round(max_count_res, -res_tick_zeros) + 1, res_tick_gap))
if how_to_scale == 'all to 100':
susc_ticks = [
0, 0.25 * max_count_susc, 0.5 * max_count_susc,
0.75 * max_count_susc, max_count_susc
]
res_ticks = [
0, 0.25 * max_count_res, 0.5 * max_count_res, 0.75 * max_count_res,
max_count_res
]
susc_ticks_labels = ['0', '25', '50', '75', '100']
res_ticks_labels = ['0', '25', '50', '75', '100']
else:
if susc_xticks is not None and susc_gap is not None:
susc_ticks_labels = [str(x) for x in susc_xticks]
susc_ticks = []
for i in susc_xticks:
if i < susc_gap[0]:
susc_ticks.append(i)
else:
susc_ticks.append(i - (susc_gap_width - plot_gap_size))
else:
susc_ticks_labels = [str(x) for x in susc_ticks]
if res_xticks is not None:
res_ticks = res_xticks
res_ticks_labels = [str(x) for x in res_ticks]
svg_lines.append(
svg.svg_line(x_susc_bar_left, y, x_centre - centre_space, y, 'black',
1))
svg_lines.append(
svg.svg_line(x_centre + centre_space, y, x_res_bar_right, y, 'black',
1))
y_tick = y
y += 5
for drug in drugs:
y_drug_top = y
for tool in tools:
if drug not in common_data.first_line_drugs and tool == '10k_predict':
continue
stats = stats_dict[drug][tool]
y_bottom = y + bar_height
if how_to_scale == 'all to 100':
if sample_count[drug]['res'] == 0:
x_fail = x_fn = x_right = x_centre + centre_space
else:
x_fail = x_centre + centre_space + res_bar_width * (
stats['UNK_R'] +
stats['FAIL_R']) / sample_count[drug]['res']
x_fn = x_fail + res_bar_width * (stats['FN'] /
sample_count[drug]['res'])
x_right = x_centre + centre_space + res_bar_width
else:
x_fail = x_centre + centre_space + res_bar_width * (
(stats['UNK_R'] + stats['FAIL_R']) / max_count_res)
x_fn = x_fail + res_bar_width * (stats['FN'] / max_count_res)
x_right = x_centre + centre_space + res_bar_width * (
sample_count[drug]['res'] / max_count_res)
svg_lines.append(
svg.svg_rectangle(x_centre + centre_space, y, x_fail, y_bottom,
common_data.other_colours['UNK_R'], 'black'))
svg_lines.append(
svg.svg_rectangle(x_fail, y, x_fn, y_bottom,
common_data.other_colours['FN'], 'black'))
svg_lines.append(
svg.svg_rectangle(x_fn, y, x_right, y_bottom,
common_data.tool_colours[tool], 'black'))
if how_to_scale == 'all to 100':
if sample_count[drug]['susc'] == 0:
x_fail = x_fn = x_right = x_centre - centre_space
else:
x_fail = x_centre - centre_space - susc_bar_width * (
(stats['UNK_S'] + stats['FAIL_S']) /
sample_count[drug]['susc'])
x_fp = x_fail - susc_bar_width * stats[
'FP'] / sample_count[drug]['susc']
x_left = x_centre - centre_space - susc_bar_width
else:
x_fail = x_centre - centre_space - susc_bar_width * (
(stats['UNK_S'] + stats['FAIL_S']) / max_count_susc)
x_fp = x_fail - susc_bar_width * (stats['FP'] / max_count_susc)
x_left = x_centre - centre_space - susc_bar_width * (
sample_count[drug]['susc'] / max_count_susc)
svg_lines.append(
svg.svg_rectangle(x_fail, y, x_centre - centre_space, y_bottom,
common_data.other_colours['UNK_S'], 'black'))
svg_lines.append(
svg.svg_rectangle(x_fp, y, x_fail, y_bottom,
common_data.other_colours['FN'], 'black'))
svg_lines.append(
svg.svg_rectangle(x_left, y, x_fp, y_bottom,
common_data.tool_colours[tool], 'black'))
y += bar_height
svg_lines.append(
svg.svg_text(x_centre,
0.5 * (y_drug_top + y),
common_data.drug_abbreviations[drug],
15,
vertical_align='middle'))
if how_to_scale == 'all to 100':
svg_lines.append(
svg.svg_text(x_susc_bar_left - 3,
0.5 * (y_drug_top + y),
str(sample_count[drug]['susc']),
15,
position='end',
vertical_align='middle'))
svg_lines.append(
svg.svg_text(x_res_bar_right + 3,
0.5 * (y_drug_top + y),
str(sample_count[drug]['res']),
15,
position='start',
vertical_align='middle'))
y += drug_spacer
grid_lines = []
for x, label in zip(res_ticks, res_ticks_labels):
x_pos = x_centre + centre_space + res_bar_width * x / max_count_res
svg_lines.append(
svg.svg_line(x_pos, y_tick - 4, x_pos, y_tick, 'black', 1))
svg_lines.append(svg.svg_text(x_pos, y_tick - 7, label, 15))
grid_lines.append(
svg.svg_line(x_pos, y_tick, x_pos, y - drug_spacer, 'lightgray',
1))
for x, label in zip(susc_ticks, susc_ticks_labels):
x_pos = x_centre - centre_space - susc_bar_width * x / max_count_susc
svg_lines.append(
svg.svg_line(x_pos, y_tick - 4, x_pos, y_tick, 'black', 1))
svg_lines.append(svg.svg_text(x_pos, y_tick - 7, label, 15))
grid_lines.append(
svg.svg_line(x_pos, y_tick, x_pos, y - drug_spacer, 'lightgray',
1))
if susc_gap is not None:
svg_lines.append(r'''<defs>
<linearGradient id="gradwhiteleft" x1="0%" y1="0%" x2="100%" y2="0%">
<stop offset="50%" style="stop-color:rgb(255,255,255);stop-opacity:-1" />
<stop offset="100%" style="stop-color:rgb(255,255,255);stop-opacity:1" />
</linearGradient>
</defs>''')
svg_lines.append(r'''<defs>
<linearGradient id="gradwhiteright" x1="0%" y1="0%" x2="100%" y2="0%">
<stop offset="50%" style="stop-color:rgb(255,255,255);stop-opacity:1" />
<stop offset="100%" style="stop-color:rgb(255,255,255);stop-opacity:-1" />
</linearGradient>
</defs>''')
x_left = x_centre - centre_space - susc_bar_width * (
(susc_gap[0] + plot_gap_size) / max_count_susc)
x_right = x_centre - centre_space - susc_bar_width * (susc_gap[0] /
max_count_susc)
x_middle = 0.5 * (x_left + x_right)
svg_lines.append(
svg.svg_rectangle(x_left,
y_tick + 1,
x_middle,
y + 1,
'url(#gradwhiteleft)',
'white',
border_width=0))
svg_lines.append(
svg.svg_rectangle(x_middle,
y_tick + 1,
x_right,
y + 1,
'url(#gradwhiteright)',
'white',
border_width=0))
svg_lines.append(
svg.svg_line(x_left + 3, y_tick, x_right, y_tick, 'white', 1))
svg_lines.append(
svg.svg_line(x_right - 3, y_tick + 3, x_right + 3, y_tick - 3,
'black', 1))
svg_lines.append(
svg.svg_line(x_left, y_tick + 3, x_left + 6, y_tick - 3, 'black',
1))
with open(outfile, 'w') as f:
print(r'''<?xml version="1.0" standalone="no"?>
<!DOCTYPE svg PUBLIC " -//W3C//DTD SVG 1.0//EN" "http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd">
<svg width="''' + str(total_width + extra_width) + '" height="' +
str(y) + '">',
file=f)
print(*grid_lines, sep='\n', file=f)
print(*svg_lines, sep='\n', file=f)
print('</svg>', file=f)
svg.svg2pdf(outfile, outfile.replace('.svg', '.pdf'))
