plot_survcurves {coda4microbiome}

plot_survcurves

Description

Plots survival curves stratifying samples based on their signature value. Signature value for stratification can be set by the user.

Usage

plot_survcurves(risk.score, time, status, strata.quantile = 0.5)

Arguments

risk.score

microbial risk score values resulting from the coda_coxnet model

time

time to event or follow up time for right censored data. Must be a vector (type:numeric) specifying time to event for each sample for right censored data (what about interval data?).

status

event occurrence. Vector (type: numeric or logical) specifying 0 or FALSE for no event occurrence, and 1 or TRUE for event occurrence.

strata.quantile

cut-off quantile (values 0, 1) for sample stratification based on signature value. Default is set to 0.5 quantile of the signature.

Value

return an object of class ggsurvplot which is list containing the following: plot: the survival plot (ggplot object). table: the number of subjects at risk table per time (ggplot object). data.survplot: data used to plot the survival curves (data.frame). data.survtable: data used to plot the tables under the main survival curves (data.frame).

Author(s)

M. Calle, M. Pujolassos, T. Susin

Examples

set.seed(12345)

data(data_survival, package = "coda4microbiome")
time <- Event_time
status <- Event
crohn_cox <- coda_coxnet(x = x,
                         time = Event_time,
                         status = Event,
                         covar = NULL,
                         lambda = "lambda.1se", nvar = NULL,
                         alpha = 0.9, nfolds = 10, showPlots = TRUE, coef_threshold = 0)
plot_survcurves(risk.score = crohn_cox$risk.score,
                 time,
                 status,
                 strata.quantile = 0.5)


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