coda4microbiome (version 0.2.4)

plot_riskscore: plot_riskscore

Description

Plots samples ordered by microbial risk score values along time to event.

Usage

plot_riskscore(risk.score, x, time, status, showPlots = TRUE)

Value

returns an object of class HeatmapList.

Arguments

risk.score

microbial risk score values resulting from the coda_coxnet model

x

original survival data

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.

status

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

showPlots

(default: TRUE)

Author

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_riskscore(risk.score = crohn_cox$risk.score,
                    x = x,
                    time = Event_time,
                    status =  Event,
                    showPlots = TRUE)


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