def draw_survival_curve(feature, surv, q=.25, std=None, **args):
feature = process_feature(feature, q, std)
fmla = robjects.Formula('Surv(days, event) ~ feature')
m = get_cox_ph(surv, feature)
r_data = m.rx2('call')[2]
# s = survival.survdiff(fmla, r_data)
# p = str(s).split('\n\n')[-1].strip().split(', ')[-1]
draw_survival_curves_mpl(survival.survfit(fmla, r_data), **args)
def plot_me(sub_f, label):
if (get_vec_type(sub_f) == 'real') and (len(sub_f.unique()) > 10):
sub_f = to_quants(sub_f, q=q, std=std)
m = get_cox_ph(surv, sub_f, formula=fmla)
r_data = m.rx2('call')[2]
p = log_rank(sub_f, surv)['p']
ls = r.c(*colors)
r.plot(survival.survfit(fmla, r_data), lty=1, col=ls, lwd=4, cex=1.25,
xlab='Years to Event', ylab='Survival');
r.title(label, cex=3.)
if ann == 'p':
r.text(.2, 0, labels='logrank p = {0:.1e}'.format(p), pos=4)
elif ann != None:
r.text(0, labels=ann, pos=4)
def plot_me(sub_f, label):
if (get_vec_type(sub_f) == 'real') and (len(sub_f.unique()) > 10):
sub_f = to_quants(sub_f, q=q, std=std)
m = get_cox_ph(surv, sub_f, formula=fmla)
r_data = m.rx2('call')[2]
p = log_rank(sub_f, surv)['p']
ls = r.c(*colors)
r.plot(survival.survfit(fmla, r_data),
lty=1,
col=ls,
lwd=4,
cex=1.25,
xlab='Years to Event',
ylab='Survival')
r.title(label, cex=3.)
if ann == 'p':
r.text(.2, 0, labels='logrank p = {0:.1e}'.format(p), pos=4)
elif ann != None:
r.text(0, labels=ann, pos=4)