jdp {varoc}

JDP: jittered ot plot

Description

Jittered dot plot to visualize classification and continuity performances of biomarkers.

Usage

jdp(fit,
min=NULL,max=NULL,eps=0.2,seed=1,
main="JDP",ylab="x",xlab=c("y=0","y=1"),
col=c("blue","red","gray","gray"),
legend="top",lwd=1,lty=3,
cex.main=1,cex.pt=1.5,cex.lab=1,cex.axis=1,cex.legend=1,digits=2)

Arguments

fit

fitted results from the amd() function in the varoc R package.

min

minimum value of y-axis.

max

maximum value of y-axis.

eps

jittered range of x-axis.

seed

seed number for jittering x-axis.

main

title for the plot

ylab

title for the y axis.

xlab

title for the x axis.

col

colors to true positive, false negative, false positive, false negative.

legend

legend location, "bottomright", "bottom", "bottomleft", "left", "topleft", "top", "topright", "right" and "center".

lwd

line width.

lty

line type.

cex.main

main size.

cex.pt

point size.

cex.lab

label size.

cex.axis

axis size.

cex.legend

legend size.

digits

number of decimals.

Details

The jdp function plots biomarker (or x) by jittered x-axis (y=0 vs y=1) and visualizes its classification and continuity metrics. The vertical dotted line is the threshold corresponding to FPF=fpf, and the two horizontal lines at y=0 and y=1 are false positive and true positive means, respectively. See the amd function for more details.

Value

No return value, called for side effects.

Author(s)

Yunro Chung [aut, cre]

References

Danielle Brister and Yunro Chung, Value added receiver operating characteristics curve (in-progress)

Examples

set.seed(1)

n1=50
n0=50

#1. marker 1 (useless biomaker)
y1=c(rep(1,n1),rep(0,n0))
x1=abs(c(rnorm(n1,0,1),rnorm(n0,0,1)))

#1.1.amd
fit1=amd(y=y1,x=x1,fpf=0.3)
print(fit1)

#1.2. varoc
varoc(fit1)

#1.3. jdp
jdp(fit1)

#2. marker 2 (useful biomarker)
y2=y1
x2=abs(c(rnorm(n1,1,1),rnorm(n0,0,1)))

#2.1. amd
fit2=amd(y=y2,x=x2,fpf=0.3)

#2.2. varoc for marker 1 vs marker 2
mzr.min=min(c(fit1$res$amd,fit2$res$amd))
mzr.max=max(c(fit1$res$amd,fit2$res$amd))

varoc(fit1,mzr="AMD",mzr.min=mzr.min,mzr.max=mzr.max)
varoc(fit2,mzr="AMD",mzr.min=mzr.min,mzr.max=mzr.max)

#2.3. varoc for marker 1 vs marker 2
min=min(c(x1,x2))
max=max(c(x1,x2))
jdp(fit1,min=min,max=max)
jdp(fit2,min=min,max=max)