antennaPlot.fn {CGManalyzer}

draw an antenna plot

Description

function to draw an antenna plot

Usage

antennaPlot.fn(Mean, SSMD, Name, CIlower, CIupper, xRange = NA, yRange = NA,
col = 1:length(Mean), pch = 1:length(Mean), cex = 1, Position = "topleft", main = "")

Arguments

Mean

vector for mean difference in a comparison

SSMD

vector for strictly standardized mean difference (ssmd) in a comparison

Name

vector for name of pairs in a comparison

CIlower

vector for the lower bound of confidence interval

CIupper

vector for the upper bound of confidence interval

xRange

pre-defined range for the x-axis if needed

yRange

pre-defined range for the y-axis if needed

col

vector of colors for pairs in a comparison

pch

vector of point types for pairs in a comparison

cex

cex for the legend

Position

position indicating where to put the legend, such as 'topleft'

main

title name

Details

a function to draw an antenna plot, namely, plot ssmd vs. mean difference with confidence interval.

Value

no return value

Author(s)

Xiaohua Douglas Zhang

References

Zhang XD, Zhang Z, Wang D. 2018. CGManalyzer: an R package for analyzing continuous glucose monitoring studies. Bioinformatics 34(9): 1609-1611 (DOI: 10.1093/bioinformatics/btx826).

Examples

library(CGManalyzer)
package.name <- "CGManalyzer"
source( system.file("SPEC", "SPECexample.R", package = package.name) )
scalesInTime <- Scales*equal.interval
pvalSSMD.mat <- read.csv(file=system.file("SPEC", "pvalSSMD.csv", package = package.name),
              row.names=1)
outNames <- dimnames(pvalSSMD.mat)[[2]]
SSMD.mat <- as.matrix( pvalSSMD.mat[, substring(outNames, 1, 4) == "SSMD"] )
mDiff.mat <- as.matrix(pvalSSMD.mat[, substring(outNames, 1, 5) == "mDiff"])
CIlower.mat <- as.matrix(pvalSSMD.mat[, substring(outNames, 1, 7) == "CIlower"])
CIupper.mat <- as.matrix(pvalSSMD.mat[, substring(outNames, 1, 7) == "CIupper"])
pairNames <- gsub("mDiff_", "", dimnames(mDiff.mat)[[2]], fixed=TRUE)
idx = 1:4
xRange <- range( c( range( CIlower.mat[idx,], na.rm=TRUE), 0,
      range( CIupper.mat[idx,], na.rm=TRUE) )  )
yRange <- range( c(0, range( SSMD.mat[idx,], na.rm=TRUE ) ) )
par(mfrow=c(2,2))
for( i in idx ) {
    Main <- paste0("Sample entropy at a scale of ", scalesInTime[i], " ", timeUnit, "s")
    condt <- !is.na(mDiff.mat[i,]) & !is.na(SSMD.mat[i,])
	antennaPlot.fn(Mean=mDiff.mat[i,condt], SSMD=SSMD.mat[i, condt], Name = pairNames[condt],
	            CIlower=CIlower.mat[i,condt], CIupper=CIupper.mat[i,condt], xRange=xRange,
	            yRange=yRange, col=1:length(pairNames[condt]), pch=1:length(pairNames[condt]),
	            cex=0.8, Position = "topleft", main = Main)
}