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Small changes to bokeh module imports in utils.plotting that were failing with Hail update #540

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merged 1 commit into from
May 10, 2023
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Small changes to bokeh module imports in utils.plotting that were failing with Hail update #540

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19 changes: 10 additions & 9 deletions gnomad/utils/plotting.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,9 +19,10 @@
Grid,
HoverTool,
Legend,
TabPanel,
Tabs,
Title,
)
from bokeh.models.widgets import Panel, Tabs
from bokeh.palettes import Spectral8, d3, viridis # pylint: disable=no-name-in-module
from bokeh.plotting import figure
from bokeh.transform import factor_cmap
Expand Down Expand Up @@ -113,7 +114,7 @@ def plot_hail_hist(
line_color: str = "#033649",
hover_mode: str = "mouse",
hide_zeros: bool = False,
) -> bokeh.plotting.Figure:
) -> bokeh.plotting.figure:
"""
Plot histogram from Hail hist aggregation.

Expand Down Expand Up @@ -152,7 +153,7 @@ def plot_multi_hail_hist(
hover_mode: str = "mouse",
hide_zeros: bool = False,
alpha: float = None,
) -> bokeh.plotting.Figure:
) -> bokeh.plotting.figure:
"""
Plot multiple histograms on the same plot.

Expand Down Expand Up @@ -273,7 +274,7 @@ def plot_hail_hist_cumulative(
line_width: int = 3,
log: bool = False,
hover_mode: str = "mouse",
) -> bokeh.plotting.Figure:
) -> bokeh.plotting.figure:
"""
Plot cumulative histogram from Hail hist aggregation.

Expand Down Expand Up @@ -319,7 +320,7 @@ def plot_hail_hist_both(
hist_data, f"{title} (Cumulative)", normalize, log=log
)
return Tabs(
tabs=[Panel(child=p1, title="Raw"), Panel(child=p2, title="Cumulative")]
tabs=[TabPanel(child=p1, title="Raw"), TabPanel(child=p2, title="Cumulative")]
)


Expand All @@ -339,15 +340,15 @@ def linear_and_log_tabs(plot_func: Callable, **kwargs) -> Tabs: # noqa: D103
panels = []
for axis_type in ["linear", "log"]:
fig = plot_func(**kwargs, axis_type=axis_type)
panel = Panel(child=fig, title=axis_type)
panel = TabPanel(child=fig, title=axis_type)
panels.append(panel)

return Tabs(tabs=panels)


def plot_hail_file_metadata(
t_path: str,
) -> Optional[Union[Grid, Tabs, bokeh.plotting.Figure]]:
) -> Optional[Union[Grid, Tabs, bokeh.plotting.figure]]:
"""
Take path to hail Table or MatrixTable (gs://bucket/path/hail.mt), output Grid or Tabs, respectively.

Expand Down Expand Up @@ -581,8 +582,8 @@ def plot_hail_file_metadata(

return Tabs(
tabs=[
Panel(child=entries_grid, title="Entries"),
Panel(child=rows_grid, title="Rows"),
TabPanel(child=entries_grid, title="Entries"),
TabPanel(child=rows_grid, title="Rows"),
]
)
else:
Expand Down