get_channels_colors (channels:pandas.core.frame.DataFrame, events:pandas.core.frame.DataFrame, participant_id:int=None, array_index:int=None, time_range:Tuple[str,str]=None, event_filter:Iterable[str]=None, palette:str='muted')
plot_sleep_channels (channels:pandas.core.frame.DataFrame, x:str='collection_timestamp', y:str='values', row:str='source', hue:str='channel_group', participant_id:int=None, array_index:int=None, time_range:Tuple[str,str]=None, y_include:Iterable[str]=None, y_exclude:Iterable[str]=None, rename_channels:dict={'actigraph': 'Actigraph', 'body_position': 'Body Position', 'heart_rate': 'Heart Rate', 'heart_rate_raw': 'Heart Rate Raw', 'pat_infra': 'PAT Infra', 'pat_amplitude': 'PAT Amplitude', 'pat_lpf': 'PAT LPF', 'respiratory_movement': 'Respiratory Mov.', 'spo2': 'SpO2', 'snore_db': 'Snore dB', 'pat_view': 'PAT View', 'sleep_stage': 'Sleep Stage'}, discrete_events:Iterable[str]=['sleep_stage', 'body_position'], resample:str='1s', color_map:pandas.core.series.Series=None, palette:str='muted', fig:pheno_utils.timeseries_plot s.TimeSeriesFigure=None, ax:List[matplotlib.axes._axes.Axes]=None, height=1, **kwargs)
plot channels data for a given participant and array_index
plot_sleep (events:pandas.core.frame.DataFrame, channels:pandas.core.frame.DataFrame, participant_id:int=None, array_index:int=None, time_range:Tuple[str,str]=None, event_filter:Iterable[str]=None, channel_filter:Iterable[str]=['actigraph', 'pat_infra', 'body_position', 'snore_db', 'heart_rate', 'spo2'], event_height:float=1, channel_height:float=0.5, padding:float=-0.02, figsize:Tuple[float,float]=None, palette:str='muted')
*Plot sleep events and channels data.
Args:
events (pd.DataFrame): The sleep events dataframe.
channels (pd.DataFrame): The sleep channels dataframe.
participant_id (int): The participant id to filter the data.
array_index (int): The array index to filter the data.
time_range (Tuple[str, str]): The time range to filter the data.
event_filter (Iterable[str]): The events to include in the plot.
channel_filter (Iterable[str]): The channels to include in the plot.
event_height (float): The relative height of the events subplot.
channel_height (float): The relative height of each channel's subplot.
padding (float): The padding between subplots.
figsize (Tuple[float, float]): The size of the figure.
palette (str): The color palette to use.Returns:
TimeSeriesFigure: The figure with the sleep events and channels data.*get_sleep_period (events:pandas.core.frame.DataFrame)
*Get the sleep period from the sleep events dataframe.
Args:
events (pd.DataFrame): The sleep events dataframe.Returns:
pd.DataFrame: The sleep period dataframe.*This module provides functions for plotting sleep events and channels data.
First, we will load time series DFs from the sleep monitoring dataset.
from pheno_utils import PhenoLoader
pl = PhenoLoader('sleep')
channels_df = pl.load_bulk_data('channels_time_series') # contains: heart_rate, spo2, respiratory_movement
events_df = pl.load_bulk_data('events_time_series')/home/ec2-user/projects/pheno-utils/pheno_utils/pheno_loader.py:610: UserWarning: No date field found
warnings.warn(f'No date field found')channels_df.head(5)| values | ||||||
|---|---|---|---|---|---|---|
| participant_id | cohort | research_stage | array_index | collection_timestamp | source | |
| 0 | 10k | 00_00_visit | 1 | 2020-06-23 00:40:29+03:00 | heart_rate | 62.0 |
| respiratory_movement | 0.0 | |||||
| spo2 | NaN | |||||
| 2020-06-23 00:40:29.200000+03:00 | respiratory_movement | 0.0 | ||||
| 2020-06-23 00:40:29.400000+03:00 | respiratory_movement | 0.0 |
events_df.head(5)| event_end | event | channel | start | end | |||||
|---|---|---|---|---|---|---|---|---|---|
| participant_id | cohort | research_stage | array_index | collection_timestamp | |||||
| 0 | 10k | 00_00_visit | 1 | 2020-06-23 00:40:29+03:00 | 2020-06-23 00:40:34+03:00 | Excluded | heart_rate_raw | 0 | 5 |
| 2020-06-23 00:40:29+03:00 | 2020-06-23 00:40:34+03:00 | Excluded | spo2 | 0 | 5 | ||||
| 2020-06-23 00:40:29+03:00 | 2020-06-23 00:55:29+03:00 | Wake | actigraph | 0 | 900 | ||||
| 2020-06-23 00:40:29+03:00 | 2020-06-23 00:40:34+03:00 | Invalid Time | general | 0 | 5 | ||||
| 2020-06-23 00:40:29+03:00 | 2020-06-23 00:40:32+03:00 | Artifact | pat_infra | 0 | 3 |
import seaborn as sns
sns.set_style('whitegrid')
plot_sleep(events_df, channels_df,
channel_filter=['heart_rate', 'spo2', 'respiratory_movement'],
figsize=(8, 8), padding=0.03)