KMF legend labels do not play nice with LaTeX

[spacecowboy]

The labels "_upper_0.95" and "_lower_0.95" break plotting if LaTeX is enabled:

import matplotlib as mpl
mpl.rcParams['text.usetex']=True

# Create a kaplan-meier fitter then plot...
kmf.plot(ax=ax, c="#A60628", ci_force_lines=True)

The problem is that LaTeX hates underscores... The text might also look bad if matplotlib interprets the legend as mathmode (not sure if it does). One could imagine something like this:

import matplotlib as mpl

# No more underscores
label = "{} upper 0.95".format(actual_label)
# If TeX, wrap in a text environment
if mpl.rcParams['text.usetex']:
    label = "\text{%s}" % label

[CamDavidsonPilon]

Hm, is this also a Pandas problem? That is, if I have Latex enabled, and underscores in a dataframe's column name, does that break Pandas .plot too?

[spacecowboy]

Yes it would seem that it is. Loading a csv-file with pandas, and calling plot on the dataframe results in:

/usr/local/lib/python3.4/site-packages/IPython/core/formatters.py:239: FormatterWarning: Exception in image/png formatter: LaTeX was not able to process the following string: 'study_id,id'

But the difference is that I can change the column names in the dataframe. The "_upper_0.95" is not as easily changed.

[CamDavidsonPilon]

True, that's a change I can (and will) make. Thanks!

[spacecowboy]

Great!

[CamDavidsonPilon]

@spacecowboy, I added an API to change the labels:

    kmf = KaplanMeierFitter()
    ci_labels = ['upper', 'lower']
    kmf.fit(T, ci_labels=ci_labels)
    print kmf.confidence_interval_.columns
   #['upper', 'lower']

Run a

    pip install --upgrade --no-deps git+https://github.com/CamDavidsonPilon/lifelines.git

to pull master.