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"""Script from plannotate edited to work with bokeh 3.""" | ||
from math import pi | ||
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from bokeh.models import ColumnDataSource, HoverTool, Range1d, WheelZoomTool | ||
from bokeh.models.annotations import Label | ||
from bokeh.plotting import figure | ||
import numpy as np | ||
import pandas as pd | ||
from plannotate.bokeh_plot import calc_glyphs, calc_level, calc_num_markers | ||
import plannotate.resources as rsc | ||
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def get_bokeh(df, linear=False): | ||
"""Get bokeh from plannotate updated to use Bokeh v3 to match ezcharts.""" | ||
# df = df.fillna("") | ||
x = 0 | ||
y = 0 | ||
baseradius = .18 | ||
tooltips = """ | ||
<font size="4"><b>@Feature</b> — @Type @pi_permatch_int</font><br> | ||
@Description | ||
""" # noqa: E501 | ||
hover = HoverTool(tooltips=tooltips) | ||
plotsize = .35 | ||
plotdimen = 800 | ||
x_range = Range1d(-plotsize, plotsize, bounds=(-.5, .5), min_interval=.1) | ||
y_range = Range1d(-plotsize, plotsize, bounds=(-.5, .5), min_interval=.1) | ||
toolbar = "right" | ||
p = figure( | ||
height=plotdimen, width=plotdimen, title="", | ||
toolbar_location=toolbar, toolbar_sticky=False, | ||
match_aspect=True, | ||
sizing_mode='scale_width', tools=['save', 'pan'], | ||
x_range=x_range, y_range=y_range) | ||
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# x_range=(-plotsize, plotsize), y_range=(-plotsize, plotsize)) | ||
p.toolbar.logo = None | ||
p.add_tools(WheelZoomTool(zoom_on_axis=False)) | ||
p.toolbar.active_scroll = p.select_one(WheelZoomTool) | ||
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# backbone line | ||
p.circle( | ||
x=x, y=y, radius=baseradius, line_color="#000000", | ||
fill_color=None, line_width=2.5) | ||
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df = calc_level(df) | ||
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if linear: | ||
line_length = baseradius / 5 | ||
p.line( | ||
[0, 0], [baseradius - line_length, baseradius + line_length], | ||
line_width=4, level="overlay", line_color="black") | ||
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df['pi_permatch_int'] = df['pi_permatch'].astype('int') | ||
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df['pi_permatch_int'] = df['pi_permatch_int'].astype(str) + "%" | ||
# removes percent from infernal hits | ||
df.loc[df['db'] == "Rfam", 'pi_permatch_int'] = "" | ||
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df['rstart'] = ((df["qstart"]/df["qlen"])*2*pi) | ||
df['rend'] = ((df["qend"]/df["qlen"])*2*pi) | ||
df['rstart'] = np.where( | ||
df['rstart'] < 0, df['rstart'] + (2*pi), df['rstart']) | ||
df['rend'] = np.where(df['rend'] < 0, df['rend'] + (2*pi), df['rend']) | ||
df['rend'] = np.where( | ||
df['rend'] < df['rstart'], df['rend'] + (2*pi), df['rend']) | ||
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df['Type'] = df['Type'].str.replace('rep_origin', 'origin of replication') | ||
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# DDE0BD | ||
# C97064 | ||
# C9E4CA | ||
fullcolordf = pd.read_csv( | ||
rsc.get_resource("data", "colors.csv"), index_col=0) | ||
fragcolordf = fullcolordf.copy() | ||
fragcolordf[['fill_color', 'line_color']] = fragcolordf[ | ||
['line_color', 'fill_color']] | ||
fragcolordf["fill_color"] = "#ffffff" | ||
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full = df[df["fragment"] == False] # noqa | ||
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full = full.merge( | ||
fullcolordf, | ||
how="left", on=["Type"]) | ||
full['legend'] = full['Type'] | ||
full = full.fillna( | ||
{"color": "grey", | ||
"fill_color": "#808080", | ||
"line_color": "#000000"}) | ||
frag = df[df["fragment"]] | ||
frag = frag.merge(fragcolordf, how="left", on=["Type"]) | ||
frag = frag.fillna( | ||
{"color": "grey", | ||
"fill_color": "#ffffff", | ||
"line_color": "#808080"}) | ||
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df = full.append(frag).reset_index(drop=True) | ||
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# add orientation column | ||
orient = pd.read_csv( | ||
rsc.get_resource("data", "feature_orientation.csv"), | ||
header=None, names=["Type", "has_orientation"]) | ||
orient['Type'] = orient['Type'] | ||
orient['has_orientation'] = orient['has_orientation'].map({"T": True}) | ||
df = df.merge(orient, on="Type", how="left") | ||
df['Type'] = df['Type'].str.replace("_", " ") | ||
df['has_orientation'] = df['has_orientation'].fillna(value=False) | ||
df[[ | ||
'x', 'y', "Lx1", "Ly1", | ||
"annoLineColor", "lineX", | ||
"lineY", "theta", "text_align"]] = df.apply(calc_glyphs, axis=1) | ||
df['legend'] = df['Type'] | ||
# allowedtypes = ['CDS',"promoter","origin of replication","swissprot"] | ||
allowedtypes = fullcolordf['Type'] | ||
mask = ~df['legend'].isin(allowedtypes) | ||
df.loc[mask, 'legend'] = 'misc feature' | ||
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# plot annotations | ||
source = ColumnDataSource(df) | ||
hover_labels = p.patches( | ||
'x', 'y', fill_color='fill_color', line_color='line_color', | ||
name="features", line_width=2.5, | ||
source=source, legend_group="legend") | ||
p.multi_line( | ||
xs="lineX", ys="lineY", line_color="annoLineColor", | ||
line_width=3, level="overlay", | ||
line_cap='round', alpha=.5, source=source) | ||
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# `text_align` cannot read from `source` -- have to do this workaround | ||
right = ColumnDataSource(df[df['text_align'] == 'right']) | ||
left = ColumnDataSource(df[df['text_align'] == 'left']) | ||
bcenter = ColumnDataSource(df[df['text_align'] == 'b_center']) | ||
tcenter = ColumnDataSource(df[df['text_align'] == 't_center']) | ||
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text_level = 'overlay' | ||
p.text( | ||
x="Lx1", y="Ly1", name="2", x_offset=3, y_offset=8, | ||
text_align="left", | ||
text='Feature', level=text_level, source=right) | ||
p.text( | ||
x="Lx1", y="Ly1", name="2", x_offset=-5, y_offset=8, | ||
text_align="right", text='Feature', level=text_level, source=left) | ||
p.text( | ||
x="Lx1", y="Ly1", name="2", x_offset=0, y_offset=15, | ||
text_align="center", text='Feature', | ||
level=text_level, source=bcenter) | ||
p.text( | ||
x="Lx1", y="Ly1", name="2", x_offset=0, y_offset=0, | ||
text_align="center", | ||
text='Feature', level=text_level, source=tcenter) | ||
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# calculate chunk size(s) for drawing lines | ||
plaslen = df.iloc[0]['qlen'] | ||
ticks = calc_num_markers(plaslen) | ||
ticks_cds = ColumnDataSource(ticks) | ||
p.multi_line( | ||
xs="lineX", ys="lineY", line_color="black", line_width=2, | ||
level="underlay", line_cap='round', | ||
alpha=.5, source=ticks_cds) | ||
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right = ColumnDataSource(ticks[ticks['text_align'] == 'right']) | ||
left = ColumnDataSource(ticks[ticks['text_align'] == 'left']) | ||
bcenter = ColumnDataSource(ticks[ticks['text_align'] == 'b_center']) | ||
tcenter = ColumnDataSource(ticks[ticks['text_align'] == 't_center']) | ||
p.text( | ||
x="Lx1", y="Ly1", name="2", x_offset=3, y_offset=6, | ||
text_align="left", text='bp', alpha=.5, | ||
text_font_size='size', level=text_level, source=right) | ||
p.text( | ||
x="Lx1", y="Ly1", name="2", x_offset=-5, | ||
y_offset=6, text_align="right", | ||
text='bp', alpha=.5, text_font_size='size', | ||
level=text_level, source=left) | ||
p.text( | ||
x="Lx1", y="Ly1", name="2", x_offset=0, y_offset=15, | ||
text_align="center", text='bp', alpha=.5, | ||
text_font_size='size', level=text_level, source=bcenter) | ||
p.text( | ||
x="Lx1", y="Ly1", name="2", x_offset=0, y_offset=-3, | ||
text_align="center", text='bp', alpha=.5, | ||
text_font_size='size', level=text_level, source=tcenter) | ||
p.add_tools(hover) | ||
p.add_layout(Label( | ||
x=0, y=0, name="2", x_offset=0, y_offset=-8, | ||
text_align="center", | ||
text=f"{plaslen} bp", text_color="#7b7b7b", | ||
text_font_size='16px', level=text_level)) | ||
p.hover.renderers = [hover_labels] | ||
p.axis.axis_label = None | ||
p.axis.visible = False | ||
p.grid.grid_line_color = "#EFEFEF" | ||
p.outline_line_color = "#DDDDDD" | ||
p.legend.location = 'bottom_left' | ||
p.legend.border_line_color = "#EFEFEF" | ||
p.legend.visible = True | ||
return p |
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