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2 column layout, gene rectangle colour change #143

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Merged
merged 1 commit into from
Apr 2, 2024
Merged

2 column layout, gene rectangle colour change #143

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3 changes: 3 additions & 0 deletions tsqc/__main__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -59,6 +59,9 @@ def show(page_name):
opts.Bars(color=config.PLOT_COLOURS[0], line_color=config.PLOT_COLOURS[2]),
opts.Segments(color=config.PLOT_COLOURS[2]),
opts.Curve(color=config.PLOT_COLOURS[2]),
opts.Rectangles(
fill_color=config.PLOT_COLOURS[0], line_color=config.PLOT_COLOURS[2]
),
)
logger.info(f"Showing page {page_name}")
yield pn.indicators.LoadingSpinner(value=True, width=50, height=50)
Expand Down
39 changes: 17 additions & 22 deletions tsqc/pages/mutations.py
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,6 @@ def make_muts_panel(log_y, tsm):
filtered.opts(
color="num_inheritors",
alpha="num_inheritors",
colorbar=True,
cmap="BuGn",
colorbar_position="left",
clabel="inheritors",
Expand Down Expand Up @@ -125,9 +124,8 @@ def get_mut_data(x_range, y_range, index):
def update_pop_freq_plot(x_range, y_range, index):
if not index:
return hv.Bars([], "population", "frequency").opts(
width=int(int(config.PLOT_WIDTH) / 2),
height=400,
title="Tap on a mutation",
title="Population frequencies",
default_tools=[],
tools=["hover"],
)

Expand All @@ -143,37 +141,31 @@ def update_pop_freq_plot(x_range, y_range, index):
"frequency": [mut_data[col] for col in pops],
}
)

bars = hv.Bars(df, "population", "frequency").opts(
width=int(int(config.PLOT_WIDTH) / 2),
height=400,
framewise=True,
title=f"Mutation {mut_data['id']}: population frequencies",
title="Population frequencies",
ylim=(0, max(df["frequency"]) * 1.1),
xrotation=45,
tools=["hover"],
default_tools=[],
)
return bars
else:
return hv.Bars([], "population", "frequency").opts(
width=int(int(config.PLOT_WIDTH) / 2),
height=400,
title=f"No frequencies available for mutation {mut_data['id']}",
default_tools=[],
tools=["hover"],
)

def update_mut_info_table(x_range, y_range, index):
if not index:
return hv.Table([], kdims=["Detail"], vdims=["value"]).opts(
width=int(int(config.PLOT_WIDTH) / 2),
title="Tap on a mutation",
title="Tap on a mutation"
)
mut_data = get_mut_data(x_range, y_range, index)
pops = [col for col in mut_data.index if "pop_" in col]
mut_data = mut_data.drop(pops)
return hv.Table(mut_data.items(), kdims=["Column"], vdims=["Value"]).opts(
width=int(int(config.PLOT_WIDTH) / 2),
title=f"Mutation {mut_data['id']}: details",
title=f"Mutation {mut_data['id']}"
)

pop_data_dynamic = hv.DynamicMap(
Expand All @@ -183,9 +175,17 @@ def update_mut_info_table(x_range, y_range, index):
update_mut_info_table, streams=[range_stream, selection_stream]
)

layout += (pop_data_dynamic + mut_info_table_dynamic).cols(1)
tap_widgets_layout = (mut_info_table_dynamic + pop_data_dynamic).cols(1)

return pn.Column(layout.opts(shared_axes=True).cols(1))
return pn.Row(
pn.Column(layout.opts(shared_axes=True).cols(1)),
pn.panel(
tap_widgets_layout,
align="center",
sizing_mode="stretch_width",
margin=(0, 0, 0, 200),
),
)


def make_annotation_plot(tsm, genes_df):
Expand All @@ -205,9 +205,7 @@ def make_annotation_plot(tsm, genes_df):
)
genes_rects.opts(
ylabel=None,
line_color=None,
shared_axes=True,
color="maroon",
hooks=[customise_ticks],
width=config.PLOT_WIDTH,
height=100,
Expand All @@ -231,7 +229,4 @@ def page(tsm):
log_y_checkbox,
)

# mut_data = tsm.mutations_df.loc[0]
# mut_table = pn.widgets.Tabulator(mut_data.to_frame().T, height=200, width=800)

return pn.Column(plot_options, muts_panel)