plotRS: Plot risk scores of patients

In weiliu123/PCLassoCox: A protein complex-based group lasso-Cox model for accurate prognosis and risk protein complex discovery

Description

Plot risk scores of patients

Usage

plotRS(
  rs,
  y.status,
  cutoff = median(rs),
  col.dead = "#E64B35",
  col.alive = "#00A087",
  legend.position = c(0.2, 0.9)
)

Arguments

rs	Risk score of patients
y.status	A binary variable with 1 indicating that the event has occurred and 0 indicating (right) censoring.
cutoff	The cut-off that is used to divided the patients into two groups according to rs.
col.dead	The color that corresponds to 1 in y.status.
col.alive	The color that corresponds to 0 in y.status.
legend.position	Legend position.

Examples

# load data
data(GBM)
data(PCGroup)

cv.fit1 <- cv.PCLasso(x = GBM$GBM.train$Exp,
                      y = GBM$GBM.train$survData,
                      group = PCGroup,
                      nfolds = 5)

# predict risk scores of samples in GBM.test
s <- predict(object = cv.fit1, x = GBM$GBM.test$Exp, type="link",
             lambda=cv.fit1$cv.fit$lambda.min)

plotRS(rs = s, y.status = GBM$GBM.test$survData$status)

weiliu123/PCLassoCox documentation built on Dec. 23, 2021, 5:10 p.m.