ehrapy.plot.cox_ph_forestplot

ehrapy.plot.cox_ph_forestplot(edata, *, uns_key='cox_ph', labels=None, width=1200, height=600, ecolor='dimgray', size=3, marker='o', decimal=2, text_size=12, color='k', title=None)

Generates a forest plot to visualize the coefficients and confidence intervals of a Cox Proportional Hazards model.

The edata object must first be populated using the cox_ph() function. This function stores the summary table of the CoxPHFitter in the .uns attribute of edata. The summary table is created when the model is fitted using the cox_ph() function. See also: CoxPHFitter

Parameters:

• edata (EHRData | AnnData) – Data object containing the summary table from the CoxPHFitter. This is stored in the .uns attribute, after fitting the model using cox_ph().

• uns_key (str, default: 'cox_ph') – Key in .uns where cox_ph() function stored the summary table. See argument uns_key in cox_ph().

• labels (Iterable[str] | None, default: None) – List of labels for each coefficient, default uses the index of the summary table.

• width (int, default: 1200) – Plot width in pixels.

• height (int, default: 600) – Plot height in pixels.

• ecolor (str, default: 'dimgray') – Color of the error bars.

• size (int, default: 3) – Size of the markers.

• marker (str, default: 'o') – Marker style.

• decimal (int, default: 2) – Number of decimal places to display.

• text_size (int, default: 12) – Font size of the text.

• color (str, default: 'k') – Color of the markers.

• title (str | None, default: None) – Set the title of the plot.

Return type:

Overlay | None

Returns:

HoloViews Overlay with forest plot and text annotations.

Examples

>>> import ehrdata as ed
>>> import ehrapy as ep
>>> edata = ed.dt.mimic_2()[
...     :, ["mort_day_censored", "censor_flg", "gender_num", "afib_flg", "day_icu_intime_num"]
... ]
>>> coxph = ep.tl.cox_ph(edata, event_col="censor_flg", duration_col="mort_day_censored")
>>> ep.pl.cox_ph_forestplot(edata)