def test_Square() -> None:
marker = Square()
check_marker_properties(marker)
check_line_properties(marker)
check_fill_properties(marker)
check_hatch_properties(marker)
check_properties_existence(marker, MARKER, LINE, FILL, HATCH, GLYPH, ["marker"])
def test_Square():
marker = Square()
assert marker.angle == "angle"
yield check_marker, marker
yield check_fill, marker
yield check_line, marker
yield check_props, marker, ["angle"], MARKER, FILL, LINE
def test_Square() -> None:
marker = Square()
check_marker_properties(marker)
check_fill_properties(marker)
check_line_properties(marker)
check_properties_existence(marker, MARKER, FILL, LINE, GLYPH)
def test_Square():
marker = Square()
yield check_marker_properties, marker
yield check_fill_properties, marker
yield check_line_properties, marker
yield check_properties_existence, marker, MARKER, FILL, LINE, GLYPH
def mann_only_interactive(data,
cut1,
cut2,
chrs_plot=None,
ms=6,
color_sequence=['#7fc97f', "#beaed4", '#fdc086']):
'''
Generate interactive dots.
:param data:
:param cut1:
:param cut2:
:param ms: Marker size. Default 6.
:return:
'''
# Defining DataFrame for bokeh
ts = DataFrame({
'snp': data['snp'],
'pos': data['pos'],
'chr': data['chr'],
'color': np.zeros(len(data), dtype='S20'),
'abspos': data['pos'],
'pval1': -np.log10(data['pval1']),
'pval1_q': -np.log10(data['pval1_q']),
'pval2': -np.log10(data['pval2']),
'pval2_q': -np.log10(data['pval2_q'])
})
# Calculating proper positions
if chrs_plot is None:
chrs = np.unique(ts['chr'])
if type(chrs[0]) == str:
chrs = sorted_nicely(chrs)
else:
chrs.sort()
else:
chrs = chrs_plot
print(chrs)
temp_pos = 0
xtixks_pos = np.zeros(len(chrs) + 1)
print(chrs)
for i in range(len(chrs)):
# Can be optimized here
temp = ts['abspos'][ts['chr'] == chrs[i]]
if len(temp) > 0:
temp = np.max(temp)
else:
temp = 1000
print(temp)
xtixks_pos[i + 1] = temp
# temp_pos += temp
# xtixks_pos[i+1] = temp_pos
# ts['abspos'][ts['chr'] == chrs[i+1]] += temp_pos
print(xtixks_pos)
xtixks_pos = np.cumsum(xtixks_pos)
print(xtixks_pos)
for i in range(len(chrs)):
ts['abspos'][ts['chr'] == chrs[i]] += xtixks_pos[i]
print(xtixks_pos)
xtixks_pos = (xtixks_pos[1:] + xtixks_pos[:-1]) / 2.0
print(xtixks_pos)
print(chrs)
# Old color selection
# for i in range(len(chrs)):
# if i % 2 == 0:
# ts['color'][ts['chr'] == chrs[i]] = '#FA8072'
# else:
# ts['color'][ts['chr'] == chrs[i]] = '#00BFFF'
for i in range(len(chrs)):
ts['color'][ts['chr'] == chrs[i]] = color_sequence[i %
len(color_sequence)]
# Defining hover tools
hover1 = HoverTool(tooltips=[
("chr", "@chr"),
("snp", "@snp"),
("pos", "@pos"),
("-log10(pval1,pval2)", "(@pval1, @pval2)"),
])
hover2 = HoverTool(tooltips=[
("chr", "@chr"),
("snp", "@snp"),
("pos", "@pos"),
("-log10(pval1,pval2)", "(@pval1, @pval2)"),
])
hoverq = HoverTool(tooltips=[
("chr", "@chr"),
("snp", "@snp"),
("pos", "@pos"),
("-log10(pval1,pval2)", "(@pval1, @pval2)"),
])
tools1 = ['reset', 'xwheel_zoom', 'xpan', 'box_select', hover1]
tools2 = ['reset', 'xwheel_zoom', 'xpan', 'box_select', hover2]
toolsq = ['reset', 'wheel_zoom', 'pan', 'box_select', hoverq]
source = ColumnDataSource(data=ts)
# original_source = ColumnDataSource(data=ts)
source_filt = ColumnDataSource(
data=dict(snp=[], pos=[], pval1=[], pval2=[]))
source.callback = CustomJS(args=dict(source_filt=source_filt),
code="""
var inds = cb_obj.get('selected')['1d'].indices;
var d1 = cb_obj.get('data');
var d2 = source_filt.get('data');
d2['snp'] = []
d2['pos'] = []
d2['chr'] = []
d2['pval1'] = []
d2['pval2'] = []
for (i = 0; i < inds.length; i++) {
d2['snp'].push(d1['snp'][inds[i]])
d2['pos'].push(d1['pos'][inds[i]])
d2['chr'].push(d1['chr'][inds[i]])
d2['pval1'].push(d1['pval1'][inds[i]])
d2['pval2'].push(d1['pval2'][inds[i]])
}
source_filt.trigger('change');
// data_table_filt.trigger('change');
""")
selection_glyph = Circle(fill_color='firebrick', line_color=None, size=ms)
nonselection_glyph = Circle(fill_color='gray',
fill_alpha=0.1,
line_color=None,
size=ms)
selection_glyph_2 = Square(fill_color='firebrick',
line_color=None,
size=ms)
nonselection_glyph_2 = Square(fill_color='gray',
fill_alpha=0.1,
line_color=None,
size=ms)
upper_bound = np.ceil(
np.max([np.max(ts['pval1']), np.max(ts['pval2'])]) + .51)
p1 = figure(responsive=True,
plot_width=900,
plot_height=300,
tools=tools1,
x_range=[0, np.max(ts['abspos'])],
y_range=[-0.12 * upper_bound, upper_bound],
webgl=True)
r1 = p1.circle('abspos',
'pval1',
source=source,
line_color=None,
color='color',
size=ms)
r1.selection_glyph = selection_glyph
r1.nonselection_glyph = nonselection_glyph
p1.patch([0, np.max(ts['abspos']),
np.max(ts['abspos']), 0],
[0, 0, -np.log10(cut1), -np.log10(cut1)],
alpha=0.5,
line_color=None,
fill_color='gray',
line_width=2)
p2 = figure(responsive=True,
plot_width=900,
plot_height=300,
tools=tools2,
x_range=p1.x_range,
y_range=p1.y_range,
webgl=True)
r2 = p2.square('abspos',
'pval2',
source=source,
line_color=None,
color='color',
size=ms)
r2.selection_glyph = selection_glyph_2
r2.nonselection_glyph = nonselection_glyph_2
p2.patch([0, np.max(ts['abspos']),
np.max(ts['abspos']), 0],
[0, 0, -np.log10(cut1), -np.log10(cut1)],
alpha=0.5,
line_color=None,
fill_color='gray',
line_width=2)
pq1 = figure(responsive=True,
plot_width=400,
plot_height=400,
tools=toolsq,
webgl=True)
pq1.line([0, 7], [0, 7],
line_width=3,
color="black",
alpha=0.5,
line_dash=[4, 4])
rq1 = pq1.circle('pval1_q',
'pval1',
source=source,
line_color=None,
size=ms)
# err_x = -np.log10(np.concatenate([data['pval1_q'][:100], data['pval1_q'][100::-1]]))
# err_y = -np.log10(np.concatenate([data['pval1_q_top'][:100], data['pval1_q_bot'][100::-1]]))
# er1 = pq1.patch(err_x, err_y, alpha=0.2, color='blue')
rq2 = pq1.square('pval2_q',
'pval2',
source=source,
line_color=None,
size=ms,
color="red")
# err_x = -np.log10(np.concatenate([data['pval2_q'][:100], data['pval2_q'][100::-1]]))
# err_y = -np.log10(np.concatenate([data['pval2_q_top'][:100], data['pval2_q_bot'][100::-1]]))
# er2 = pq1.patch(err_x, err_y, alpha=0.2, color='olive')
rq1.selection_glyph = selection_glyph
rq1.nonselection_glyph = nonselection_glyph
rq2.selection_glyph = selection_glyph_2
rq2.nonselection_glyph = nonselection_glyph_2
# Labels for axes
pq1.yaxis.axis_label = "Experimental quantiles, -log10(p)"
pq1.xaxis.axis_label = "Theoretical quantiles, -log10(p)"
p1.yaxis.axis_label = "-log10(p)"
p1.xaxis.axis_label = "Chromosomes"
p2.yaxis.axis_label = "-log10(p)"
p2.xaxis.axis_label = "Chromosomes"
p1.xgrid.grid_line_color = None
p2.xgrid.grid_line_color = None
# print(xtixks_pos)
p1.xaxis[0].ticker = FixedTicker(ticks=[])
p2.xaxis[0].ticker = FixedTicker(ticks=[])
p1.text(xtixks_pos,
xtixks_pos * 0 - 0.12 * upper_bound,
[str(chrs[i]) for i in range(len(chrs))],
text_align='center')
p2.text(xtixks_pos,
xtixks_pos * 0 - 0.12 * upper_bound,
[str(chrs[i]) for i in range(len(chrs))],
text_align='center')
# p1.xaxis[0].ti
columns = [
TableColumn(field="chr", title="chr"),
TableColumn(field="snp", title="snp"),
TableColumn(field="pos", title="pos"),
TableColumn(field="pval1", title="pval1"),
TableColumn(field="pval2", title="pval2"),
]
data_table = DataTable(source=source,
columns=columns,
width=300,
height=280)
p3 = vform(data_table)
data_table_filt = DataTable(source=source_filt,
columns=columns,
width=500,
height=500)
p4 = vform(data_table_filt)
return p1, p2, p3, p4, pq1
fill_color="#B3DE69")),
]
markers = [
("circle", Circle(x="x", y="y", radius=0.1, fill_color="#3288BD")),
("circle_x",
CircleX(x="x", y="y", size="sizes", line_color="#DD1C77",
fill_color=None)),
("circle_cross",
CircleCross(x="x",
y="y",
size="sizes",
line_color="#FB8072",
fill_color=None,
line_width=2)),
("square", Square(x="x", y="y", size="sizes", fill_color="#74ADD1")),
("square_x",
SquareX(x="x",
y="y",
size="sizes",
line_color="#FDAE6B",
fill_color=None,
line_width=2)),
("square_cross",
SquareCross(x="x",
y="y",
size="sizes",
line_color="#7FC97F",
fill_color=None,
line_width=2)),
("diamond",
def test_Square():
marker = Square()
yield check_marker, marker
yield check_fill, marker
yield check_line, marker
yield check_props, marker, MARKER, FILL, LINE