superpc.rainbowplot {superpc} | R Documentation |
Make rainbow plot of superpc and compeiting predictors
Description
Makes a heatmap display of outcome predictions from superpc, along with expected survival time, and values of competing predictors.
Usage
superpc.rainbowplot(data,
pred,
sample.labels,
competing.predictors,
call.win.metafile=FALSE)
Arguments
data |
List of (test) data, of form described in superpc.train documentation |
pred |
Superpc score from superpc.predict or superpc.predict.red |
sample.labels |
Vector of sample labels of test data |
competing.predictors |
List of competing predictors to be plotted |
call.win.metafile |
Used only by Excel interface call to function |
Details
Any censored survival times are estimated by E(T|T > C), where $C$ is the observed censoring time and the Kaplan-Meier estimate from the training set is used to estimate the expectation.
Author(s)
"Eric Bair, Ph.D."
"Jean-Eudes Dazard, Ph.D."
"Rob Tibshirani, Ph.D."
Maintainer: "Jean-Eudes Dazard, Ph.D."
References
E. Bair and R. Tibshirani (2004). "Semi-supervised methods to predict patient survival from gene expression data." PLoS Biol, 2(4):e108.
E. Bair, T. Hastie, D. Paul, and R. Tibshirani (2006). "Prediction by supervised principal components." J. Am. Stat. Assoc., 101(473):119-137.
Examples
set.seed(332)
#generate some data
x <- matrix(rnorm(50*30), ncol=30)
y <- 10 + svd(x[1:50,])$v[,1] + .1*rnorm(30)
ytest <- 10 + svd(x[1:50,])$v[,1] + .1*rnorm(30)
censoring.status <- sample(c(rep(1,20), rep(0,10)))
censoring.status.test <- sample(c(rep(1,20), rep(0,10)))
featurenames <- paste("feature", as.character(1:50), sep="")
competing.predictors.test <- list(pred1=rnorm(30),
pred2=as.factor(sample(c(1,2),
replace=TRUE,
size=30)))
data <- list(x=x,
y=y,
censoring.status=censoring.status,
featurenames=featurenames)
data.test <- list(x=x,
y=ytest,
censoring.status=censoring.status.test,
featurenames=featurenames)
sample.labels <- paste("te", as.character(1:20), sep="")
a <- superpc.train(data, type="survival")
pred <- superpc.predict(a,
data,
data.test,
threshold=.25,
n.components=1)$v.pred
superpc.rainbowplot(data,
pred,
sample.labels,
competing.predictors=competing.predictors.test)