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Updating code to incorporate changes made in Bokeh v3.0.0 #4

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Updating code to incorporate changes made in Bokeh v3.0.0 #4

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665e568
Panel renamed to TabPanel in Bokeh 3.0.0
sunilnahata Feb 13, 2024
8b0ed1b
plot_width and plot_height removed in Bokeh v3.0.0
sunilnahata Feb 13, 2024
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6 changes: 3 additions & 3 deletions inucs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1945,7 +1945,7 @@ def handler_plot_command(cls, command, working_dir, chrom, start_region, end_reg
def make_heat_map(cls, matrices, chrom, start_region, end_region, output_file: Path, save_only):
from bokeh.io import show, save
from bokeh.layouts import layout
from bokeh.models import ColorBar, Panel, Tabs, Range1d, LinearColorMapper # , LogColorMapper
from bokeh.models import ColorBar, TabPanel, Tabs, Range1d, LinearColorMapper # , LogColorMapper
from bokeh.models import HoverTool, PanTool, WheelZoomTool, BoxZoomTool, ResetTool, SaveTool
from bokeh.plotting import figure, output_file as save_file
from bokeh.palettes import Greys, Oranges, Greens, Blues, Purples, Reds
Expand Down Expand Up @@ -2000,7 +2000,7 @@ def r(colors, num_colors=256): # Reverse the order going from light to dark, an
# Bokeh Bug?
# Setting match_aspect=True, aspect_scale=1 does not work for figure.rect, so setting width and height manually
figure_args = dict(
plot_width=600, plot_height=670, x_axis_location='above', toolbar_location='below',
width=600, height=670, x_axis_location='above', toolbar_location='below',
x_range=x_range, y_range=y_range, tools=tools, x_axis_label='Nucleosome 1', y_axis_label='Nucleosome 2', )

# p_overlaid = figure(
Expand Down Expand Up @@ -2064,7 +2064,7 @@ def r(colors, num_colors=256): # Reverse the order going from light to dark, an
set_fig_attr(p_norm)

lyt = layout([[p, p_norm]]) # , sizing_mode='fixed')
tabs.append(Panel(child=lyt, title=orient_label, closable=False))
tabs.append(TabPanel(child=lyt, title=orient_label, closable=False))

# # Overlaid tab
# legend_label = '' if orient == 'all' else ' (' + ','.join(Files.get_strands(orient)) + ')'
Expand Down