Skip to content

Add axes argument and return axes in plots #361

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
chinandrew wants to merge 7 commits into
base: main
Choose a base branch
from
Open

Add axes argument and return axes in plots #361

Show file tree
Hide file tree
Changes from 3 commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
6561e70
add axes argument and return axes
chinandrew Dec 4, 2020
9c146e9
fix tests
chinandrew Dec 4, 2020
516fc30
Add type annotation for ax args
chinandrew Dec 4, 2020
0877ef6
Fix docstrings
chinandrew Dec 7, 2020
96fdf31
fix argument order
chinandrew Dec 7, 2020
4097b64
Fix keyword arg
chinandrew Dec 7, 2020
edd9b81
fix limit issue
chinandrew Dec 7, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
26 changes: 15 additions & 11 deletions Python-packages/covidcast-py/covidcast/plotting.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,8 @@ def plot(data: pd.DataFrame,
time_value: date = None,
plot_type: str = "choropleth",
combine_megacounties: bool = True,
**kwargs: Any) -> figure.Figure:
ax: axes.Axes = None,
**kwargs: Any) -> axes.Axes:
"""Given the output data frame of :py:func:`covidcast.signal`, plot a choropleth or bubble map.

Projections used for plotting:
Expand Down Expand Up @@ -79,7 +80,8 @@ def plot(data: pd.DataFrame,
Defaults to `True`.
:param kwargs: Optional keyword arguments passed to ``GeoDataFrame.plot()``.
:param plot_type: Type of plot to create. Either choropleth (default) or bubble map.
:return: Matplotlib figure object.
:param ax: Optional matplotlib axis to plot on.
Copy link
Contributor

@capnrefsmmat capnrefsmmat Dec 5, 2020

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I think the docstring should say what happens if ax is not provided (axes are made, states are plotted). Maybe that goes in the text above, such as in a paragraph after the one-line summary explaining that the maps are plotted on US states by default.

Copy link
Collaborator Author

@chinandrew chinandrew Dec 7, 2020

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I think I had a bug here, the background states are always plotted and I had left that statement out. I've also added a sentence describing the return behavior.

:return: Matplotlib axes object.

"""
if plot_type not in {"choropleth", "bubble"}:
Expand All @@ -92,26 +94,27 @@ def plot(data: pd.DataFrame,
kwargs["vmax"] = kwargs.get("vmax", meta["mean_value"] + 3 * meta["stdev_value"])
kwargs["figsize"] = kwargs.get("figsize", (12.8, 9.6))

fig, ax = _plot_background_states(kwargs["figsize"])
ax = _plot_background_states(kwargs["figsize"]) if ax is None else ax
ax.axis("off")
ax.set_title(f"{data_source}: {signal}, {day_to_plot.strftime('%Y-%m-%d')}")
if plot_type == "choropleth":
_plot_choro(ax, day_data, combine_megacounties, **kwargs)
else:
_plot_bubble(ax, day_data, geo_type, **kwargs)
return fig
return ax


def plot_choropleth(data: pd.DataFrame,
time_value: date = None,
combine_megacounties: bool = True,
**kwargs: Any) -> figure.Figure:
**kwargs: Any) -> axes.Axes:
"""Plot choropleths for a signal. This method is deprecated and has been generalized to plot().
Copy link
Contributor

@capnrefsmmat capnrefsmmat Dec 5, 2020

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Want to use the deprecated directive here?

Copy link
Collaborator Author

@chinandrew chinandrew Dec 7, 2020

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

added. This also made me realize our changelog is a bit incorrect, will make another PR to fix that.


:param data: Data frame of signal values, as returned from :py:func:`covidcast.signal`.
:param time_value: If multiple days of data are present in ``data``, map only values from this
day. Defaults to plotting the most recent day of data in ``data``.
:param kwargs: Optional keyword arguments passed to ``GeoDataFrame.plot()``.
:return: Matplotlib figure object.
:return: Matplotlib axes object.
"""
warnings.warn("Function `plot_choropleth` is deprecated. Use `plot()` instead.")
return plot(data, time_value, "choropleth", combine_megacounties, **kwargs)
Expand Down Expand Up @@ -286,21 +289,22 @@ def _plot_bubble(ax: axes.Axes, data: gpd.GeoDataFrame, geo_type: str, **kwargs:
ax.legend(frameon=False, ncol=8, loc="lower center", bbox_to_anchor=(0.5, -0.1))


def _plot_background_states(figsize: tuple) -> tuple:
def _plot_background_states(figsize: tuple, ax: axes.Axes = None) -> axes.Axes:
"""Plot US states in light grey as the background for other plots.

:param figsize: Dimensions of plot.
Copy link
Contributor

@capnrefsmmat capnrefsmmat Dec 5, 2020

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

So figsize is ignored if axes are provided? Should it also be optional?

Copy link
Collaborator Author

@chinandrew chinandrew Dec 7, 2020

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

added

:return: Matplotlib figure and axes.
:param ax: Optional matplotlib axis to plot on.
:return: Matplotlib axes.
"""
fig, ax = plt.subplots(1, figsize=figsize)
ax.axis("off")
if ax is None:
fig, ax = plt.subplots(1, figsize=figsize)
state_shapefile_path = pkg_resources.resource_filename(__name__, SHAPEFILE_PATHS["state"])
state = gpd.read_file(state_shapefile_path)
for state in _project_and_transform(state, "STATEFP"):
state.plot(color="0.9", ax=ax, edgecolor="0.8", linewidth=0.5)
ax.set_xlim(plt.xlim())
ax.set_ylim(plt.ylim())
return fig, ax
return ax


def _project_and_transform(data: gpd.GeoDataFrame,
Expand Down
30 changes: 17 additions & 13 deletions Python-packages/covidcast-py/tests/test_plotting.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
from unittest.mock import patch

import matplotlib
from matplotlib import pyplot as plt
import platform
import geopandas as gpd
import numpy as np
Expand Down Expand Up @@ -49,21 +50,22 @@ def test_plot(mock_metadata):
test_county["value"] = test_county.value.astype("float")

# w/o megacounties
no_mega_fig1 = plotting.plot(test_county,
time_value=date(2020, 8, 4),
combine_megacounties=False)
plotting.plot(test_county, time_value=date(2020, 8, 4), combine_megacounties=False)
no_mega_fig1 = plt.gcf()
# give margin of +-2 for floating point errors and weird variations (1 isn't consistent)
assert np.allclose(_convert_to_array(no_mega_fig1), expected["no_mega_1"], atol=2, rtol=0)

no_mega_fig2 = plotting.plot_choropleth(test_county,
cmap="viridis",
figsize=(5, 5),
edgecolor="0.8",
combine_megacounties=False)
plotting.plot_choropleth(test_county,
cmap="viridis",
figsize=(5, 5),
edgecolor="0.8",
combine_megacounties=False)
no_mega_fig2 = plt.gcf()
assert np.allclose(_convert_to_array(no_mega_fig2), expected["no_mega_2"], atol=2, rtol=0)

# w/ megacounties
mega_fig = plotting.plot_choropleth(test_county, time_value=date(2020, 8, 4))
plotting.plot_choropleth(test_county, time_value=date(2020, 8, 4))
mega_fig = plt.gcf()
# give margin of +-2 for floating point errors and weird variations (1 isn't consistent)
assert np.allclose(_convert_to_array(mega_fig), expected["mega"], atol=2, rtol=0)

Expand All @@ -72,20 +74,22 @@ def test_plot(mock_metadata):
os.path.join(CURRENT_PATH, "reference_data/test_input_state_signal.csv"), dtype=str)
test_state["time_value"] = test_state.time_value.astype("datetime64[D]")
test_state["value"] = test_state.value.astype("float")
state_fig = plotting.plot(test_state)
plotting.plot(test_state)
state_fig = plt.gcf()
assert np.allclose(_convert_to_array(state_fig), expected["state"], atol=2, rtol=0)

# test MSA
test_msa = pd.read_csv(
os.path.join(CURRENT_PATH, "reference_data/test_input_msa_signal.csv"), dtype=str)
test_msa["time_value"] = test_msa.time_value.astype("datetime64[D]")
test_msa["value"] = test_msa.value.astype("float")
msa_fig = plotting.plot(test_msa)
plotting.plot(test_msa)
msa_fig = plt.gcf()
assert np.allclose(_convert_to_array(msa_fig), expected["msa"], atol=2, rtol=0)

# test bubble
msa_bubble_fig = plotting.plot(test_msa, plot_type="bubble")
from matplotlib import pyplot as plt
plotting.plot(test_msa, plot_type="bubble")
msa_bubble_fig = plt.gcf()
assert np.allclose(_convert_to_array(msa_bubble_fig), expected["msa_bubble"], atol=2, rtol=0)


Expand Down