Nothing
R/PlotPowerBand.R
In RHRV: Heart Rate Variability Analysis of ECG Data
Defines functions
PlotSinglePowerBand
PlotPowerBand
Documented in
PlotPowerBand
PlotSinglePowerBand
#' PlotPowerBand
#' @title Plots power determined by CalculatePowerBand function
#' @description Plots the power of the heart rate signal at different bands
#' of physiological interest.
#' @param HRVData Data structure that stores the beats register and
#' information related to it
#' @param indexFreqAnalysis Numeric parameter used to reference a particular
#' frequency analysis
#' @param normalized Plots normalized powers if TRUE
#' @param hr Plots heart rate signal if TRUE
#' @param ymax Maximum value for y axis (unnormalized plots)
#' @param ymaxratio Maximum value for y axis in LF/HF band (normalized and
#' unnormalized plots)
#' @param ymaxnorm Maximum value for y axis (normalized plots)
#' @param Tags List of tags to specify which episodes, as apnoea or oxygen
#' desaturation, are included in the plot. Tags = "all" plots all episodes present
#' in the data.
#' @param Indexes List of indexes to specify which episodes (see ListEpisodes),
#' are included in the plot. Indexes = "all" plots all episodes present
#' in the data.
#' @param Tag Deprecated argument, use Tags instead
#' @param verbose Deprecated argument maintained for compatibility, use
#' setVerbose() instead
#' @references
#' L. Rodriguez-Linares, L., A.J. Mendez, M.J. Lado, D.N. Olivieri,
#' X.A. Vila, and I. Gomez-Conde, "An open source tool for heart rate
#' variability spectral analysis", Computer Methods and Programs in
#' Biomedicine 103(1):39-50, july 2011.
#' @author M. Lado, A. Mendez, D. Olivieri, L. Rodriguez, X. Vila
#' @note See \code{\link{PlotSinglePowerBand}} for a more flexible
#' function for plotting power bands.
#' @seealso \code{\link{CalculatePowerBand}} for power calculation
#' and \code{\link{PlotSinglePowerBand}}
#' @examples
#' \dontrun{
#' # Reading a wfdb register and storing into a data structure:
#' md = CreateHRVData(Verbose = TRUE)
#' md = LoadBeatWFDB(md, RecordName = "register_name",
#' RecordPath = "register_path")
#'
#' # Calculating heart rate signal:md = BuildNIHR(md)
#'
#' # Filtering heart rate signal:
#' md = FilterNIHR(md)
#' # Interpolating heart rate signal:
#' md = InterpolateNIHR(md)
#' # Calculating spectrogram and power per band:
#' md = CreateFreqAnalysis(md)
#' md = CalculatePowerBand(md, indexFreqAnalysis = 1, size = 120,
#' shift = 10, sizesp = 1024)
#' # Plotting Power per Band
#' PlotPowerBand(md, hr = TRUE, ymax = 700000, ymaxratio = 4)
#' }
#' @keywords hplot
PlotPowerBand <-
function(HRVData, indexFreqAnalysis = length(HRVData$FreqAnalysis),
normalized = FALSE, hr = FALSE, ymax = NULL, ymaxratio = NULL,
ymaxnorm = 1, Tags=NULL, Indexes=NULL, Tag = NULL, verbose = NULL) {
# --------------------
# Plots power per band
# --------------------
# indexFreqAnalysis: index of an existing frequency analysis to use
# normalized: plots normalized powers if TRUE
# hr: plots heart rate signal if TRUE
# ymax: maximum value for y axis (unnormalized plots)
# ymaxratio: maximum value for y axis in LF/HF band (normalized and unnormalized plots)
# Tags -> Tags of episodes to include in the plot
# "all" includes all types
# Indexes -> Indexes of episodes to include in the plot
# "all" includes all episodes
HRVData = HandleVerboseArgument(HRVData, verbose)
Tags = HandleDeprecatedTagArgument(Tag = Tag, Tags = Tags)
CheckAnalysisIndex(indexFreqAnalysis, length(HRVData$FreqAnalysis),
"frequency")
Tags = CheckTags(Tags, HRVData$Episodes)
Indexes = CheckIndexes(Indexes, HRVData$Episodes)
CheckPowerBand(HRVData, indexFreqAnalysis)
VerboseMessage(HRVData$Verbose,
"Plotting power per band")
# if (is.null(ymax)) {
# ymax = max(max(HRVData$FreqAnalysis[[indexFreqAnalysis]]$ULF) , max(HRVData$FreqAnalysis[[indexFreqAnalysis]]$VLF) , max(HRVData$FreqAnalysis[[indexFreqAnalysis]]$LF) , max(HRVData$FreqAnalysis[[indexFreqAnalysis]]$HF) )
# }
# normalization
if (normalized) {
HRVData$FreqAnalysis[[indexFreqAnalysis]]$ULF=(HRVData$FreqAnalysis[[indexFreqAnalysis]]$ULF-min(HRVData$FreqAnalysis[[indexFreqAnalysis]]$ULF))/(max(HRVData$FreqAnalysis[[indexFreqAnalysis]]$ULF)-min(HRVData$FreqAnalysis[[indexFreqAnalysis]]$ULF))
HRVData$FreqAnalysis[[indexFreqAnalysis]]$VLF=(HRVData$FreqAnalysis[[indexFreqAnalysis]]$VLF-min(HRVData$FreqAnalysis[[indexFreqAnalysis]]$VLF))/(max(HRVData$FreqAnalysis[[indexFreqAnalysis]]$VLF)-min(HRVData$FreqAnalysis[[indexFreqAnalysis]]$VLF))
HRVData$FreqAnalysis[[indexFreqAnalysis]]$LF=(HRVData$FreqAnalysis[[indexFreqAnalysis]]$LF-min(HRVData$FreqAnalysis[[indexFreqAnalysis]]$LF))/(max(HRVData$FreqAnalysis[[indexFreqAnalysis]]$LF)-min(HRVData$FreqAnalysis[[indexFreqAnalysis]]$LF))
HRVData$FreqAnalysis[[indexFreqAnalysis]]$HF=(HRVData$FreqAnalysis[[indexFreqAnalysis]]$HF-min(HRVData$FreqAnalysis[[indexFreqAnalysis]]$HF))/(max(HRVData$FreqAnalysis[[indexFreqAnalysis]]$HF)-min(HRVData$FreqAnalysis[[indexFreqAnalysis]]$HF))
# HRVData$FreqAnalysis[[indexFreqAnalysis]]$LFHF=(HRVData$FreqAnalysis[[indexFreqAnalysis]]$LFHF-min(HRVData$FreqAnalysis[[indexFreqAnalysis]]$LFHF))/(max(HRVData$FreqAnalysis[[indexFreqAnalysis]]$LFHF)-min(HRVData$FreqAnalysis[[indexFreqAnalysis]]$LFHF))
VerboseMessage(HRVData$Verbose,
"Power per band normalized")
}
if (hr)
numfilas=6
else
numfilas=5
# lframes is the number of frames for plotting power per band
lframes=length(HRVData$FreqAnalysis[[indexFreqAnalysis]]$HRV)
timeAxis = HRVData$FreqAnalysis[[indexFreqAnalysis]]$Time
# Episodes
if (!is.null(Tags) || !is.null(Indexes)) {
EpisodesToPlot <- selectEpisodes(HRVData$Episodes,Tags,Indexes)
EpisodesToPlot <- EpisodesToPlot[EpisodesToPlot$selected,]
# Data for representing episodes
EpisodesAuxLeft=EpisodesToPlot$InitTime
# EpisodesAuxLeftFrame=EpisodesAuxLeft*lframes/(tail(HRVData$Beat$Time,1)-head(HRVData$Beat$Time,1)) # Beg of episodes (frames)
EpisodesAuxRight=EpisodesToPlot$InitTime + EpisodesToPlot$Duration
# EpisodesAuxRightFrame=EpisodesAuxRight*lframes/(tail(HRVData$Beat$Time,1)-head(HRVData$Beat$Time,1)) # Beg of episodes (frames)
EpisodesAuxType=EpisodesToPlot$Type
VerboseMessage(HRVData$Verbose,
paste("No of episodes:", length(EpisodesAuxLeft)))
labels <- levels(factor(EpisodesAuxType))
Pal=rainbow(length(labels))
Bor=Pal[match(EpisodesAuxType,labels)]
EpisodesLeft=HRVData$Episodes$InitTime # Beg of episodes (seconds)
#EpisodesLeftFrame=EpisodesLeft*lframes/(tail(HRVData$Beat$Time,1)-head(HRVData$Beat$Time,1)) # Beg of episodes (frames)
EpisodesRight=HRVData$Episodes$InitTime+HRVData$Episodes$Duration # Beg of episodes (seconds)
#EpisodesRightFrame=EpisodesRight*lframes/(tail(HRVData$Beat$Time,1)-head(HRVData$Beat$Time,1)) # Beg of episodes (frames)
}
previousPar = par()
par(mfrow=c(numfilas,1),omi=c(0,0,0,0),
mai=c(0,0,0,0),mar=c(3,4,1,1),
oma=c(1,0,2,0),mgp=c(1.5,.5,0))
#on.exit(par(previousPar))
# ---------- LF/HF ----------
if (is.null(ymaxratio)) {
ymaxratio = max(HRVData$FreqAnalysis[[indexFreqAnalysis]]$LFHF)
}
mfg=c(1,1,numfilas,1)
plot(timeAxis,HRVData$FreqAnalysis[[indexFreqAnalysis]]$LFHF,
type='l',xlab="",ylab="LF/HF",ylim=c(0,ymaxratio*1.1))
if (!is.null(Tags) || !is.null(Indexes)) {
EpisodesAuxTop=c(ymaxratio*1.09,ymaxratio*1.04)
EpisodesAuxBottom=c(ymaxratio*1.06,ymaxratio*1.01)
rect(EpisodesAuxLeft,EpisodesAuxBottom,
EpisodesAuxRight,EpisodesAuxTop,
border=Bor,col=Bor)
for (i in 1:length(EpisodesAuxLeft)) {
lines(rep(EpisodesAuxLeft[i],times=2),
c(0,ymaxratio*1.1),lty=2,col=Bor[i])
lines(rep(EpisodesAuxRight[i],times=2),
c(0,ymaxratio*1.1),lty=2,col=Bor[i])
}
par(xpd=NA)
legend(timeAxis[lframes/2],ymaxratio,
legend=Tags,fill=Pal,cex=0.9,ncol=length(Tags),
xjust=0.5,yjust=-0.2,bty="n")
}
VerboseMessage(HRVData$Verbose,
"Plotted LF/HF")
# ---------- ULF ----------
if (normalized==TRUE) {
ymaxv=c(0,ymaxnorm)
} else if (!is.null(ymax)) {
ymaxv=c(0,ymax)
} else {
ymaxv = c(0,max(HRVData$FreqAnalysis[[indexFreqAnalysis]]$ULF))
}
mfg=c(1,2,numfilas,1)
plot(timeAxis,
HRVData$FreqAnalysis[[indexFreqAnalysis]]$ULF,
type='l',xlab="",ylab="ULF",ylim=ymaxv)
if (!is.null(Tags) || !is.null(Indexes)) {
for (i in 1:length(EpisodesAuxLeft)) {
lines(rep(EpisodesAuxLeft[i],times=2),
c(ymaxv[1],ymaxv[2]),lty=2,col=Bor[i])
lines(rep(EpisodesAuxRight[i],times=2),
c(ymaxv[1],ymaxv[2]),lty=2,col=Bor[i])
}
}
VerboseMessage(HRVData$Verbose, "Plotted ULF")
# ---------- VLF ----------
if (normalized==TRUE) {
ymaxv=c(0,ymaxnorm)
} else if (!is.null(ymax)) {
ymaxv=c(0,ymax)
} else {
ymaxv = c(0,max(HRVData$FreqAnalysis[[indexFreqAnalysis]]$VLF))
}
mfg=c(1,3,numfilas,1)
plot(timeAxis,
HRVData$FreqAnalysis[[indexFreqAnalysis]]$VLF,
type='l',xlab="",ylab="VLF",ylim=ymaxv)
if (!is.null(Tags) || !is.null(Indexes)) {
for (i in 1:length(EpisodesAuxLeft)) {
lines(rep(EpisodesAuxLeft[i],times=2),
c(ymaxv[1],ymaxv[2]),lty=2,col=Bor[i])
lines(rep(EpisodesAuxRight[i],times=2),
c(ymaxv[1],ymaxv[2]),lty=2,col=Bor[i])
}
}
VerboseMessage(HRVData$Verbose, "Plotted VLF")
# ---------- LF ----------
if (normalized==TRUE) {
ymaxv=c(0,ymaxnorm)
} else if (!is.null(ymax)) {
ymaxv=c(0,ymax)
} else {
ymaxv = c(0,max(HRVData$FreqAnalysis[[indexFreqAnalysis]]$LF))
}
mfg=c(1,4,numfilas,1)
plot(timeAxis,
HRVData$FreqAnalysis[[indexFreqAnalysis]]$LF,type='l',xlab="",ylab="LF",ylim=ymaxv)
if (!is.null(Tags) || !is.null(Indexes)) {
for (i in 1:length(EpisodesAuxLeft)) {
lines(rep(EpisodesAuxLeft[i],times=2),
c(ymaxv[1],ymaxv[2]),lty=2,col=Bor[i])
lines(rep(EpisodesAuxRight[i],times=2),
c(ymaxv[1],ymaxv[2]),lty=2,col=Bor[i])
}
}
VerboseMessage(HRVData$Verbose, "Plotted LF")
# ---------- HF ----------
if (normalized==TRUE) {
ymaxv=c(0,ymaxnorm)
} else if (!is.null(ymax)) {
ymaxv=c(0,ymax)
} else {
ymaxv = c(0,max(HRVData$FreqAnalysis[[indexFreqAnalysis]]$HF))
}
mfg=c(1,5,numfilas,1)
texto4="Time (seconds)"
plot(timeAxis,
HRVData$FreqAnalysis[[indexFreqAnalysis]]$HF,type='l',xlab=texto4,ylab="HF",ylim=ymaxv)
if (!is.null(Tags) || !is.null(Indexes)) {
for (i in 1:length(EpisodesAuxLeft)) {
lines(rep(EpisodesAuxLeft[i],times=2),
c(ymaxv[1],ymaxv[2]),lty=2,col=Bor[i])
lines(rep(EpisodesAuxRight[i],times=2),
c(ymaxv[1],ymaxv[2]),lty=2,col=Bor[i])
}
}
VerboseMessage(HRVData$Verbose, "Plotted HF")
# ---------- HR ----------
if (numfilas==6) {
mfg=c(1,6,numfilas,1)
# lsecs is the duration of the record in seconds for plotting heart rate signal
lsecs=tail(HRVData$Beat$Time,1)-head(HRVData$Beat$Time,1)
plot(seq(head(HRVData$Beat$Time,1),tail(HRVData$Beat$Time,1),by=1/HRVData$Freq_HR),
HRVData$HR,type='l',xlab="Time (sec.)",ylab="HR (bps)")
VerboseMessage(HRVData$Verbose,"Plotted HRV")
if (!is.null(Tags) || !is.null(Indexes)) {
for (i in 1:length(EpisodesAuxLeft)) {
lines(rep(EpisodesAuxLeft[i],times=2),
c(min(HRVData$HR),max(HRVData$HR)),lty=2,col=Bor[i])
lines(rep(EpisodesAuxRight[i],times=2),
c(min(HRVData$HR),max(HRVData$HR)),lty=2,col=Bor[i])
}
#rect(EpisodesAuxLeft,rep(min(HRVData$HR),times=length(EpisodesAuxLeft)),EpisodesAuxRight,rep(max(HRVData$HR),times=length(EpisodesAuxLeft)),border=Bor)
}
# --------------------
}
if ( !is.null(Tags) || !is.null(Indexes) ) {
VerboseMessage(HRVData$Verbose, "Episodes plotted")
}
if ((normalized == TRUE) && (numfilas == 6))
title(main="Normalized power bands of HRV and Heart Rate Signal",outer=TRUE)
else if ((normalized == FALSE) && (numfilas == 6))
title(main="Power bands of HRV and Heart Rate Signal",outer=TRUE)
else if ((normalized == TRUE) && (numfilas != 6))
title(main="Normalized power bands of HRV",outer=TRUE)
else
title(main="Power bands of HRV",outer=TRUE)
VerboseMessage(HRVData$Verbose, "Power per band plotted")
#restore previous graphical parameters
par(mfrow=previousPar$mfrow, omi=previousPar$omi, mai=previousPar$mai,
mar=previousPar$mar,oma=previousPar$oma,mgp=previousPar$mgp)
}
#' PlotSinglePowerBand
#' @description Plots a concrete power band computed by the CalculatePowerBand
#' function
#' @param HRVData Data structure that stores the beats register and
#' information related to it
#' @param indexFreqAnalysis Numeric parameter used to reference a particular
#' frequency analysis
#' @param band The frequency band to be plotted. Allowd bands are "ULF", "VLF", "LF"
#' (default), "HF" and "LF/HF")
#' @param normalized Plots normalized powers if TRUE
#' @param main A main title for the plot.
#' @param xlab A label for the x axis.
#' @param ylab A label for the y axis
#' @param type 1-character string giving the type of plot desired. See
#' \code{\link[graphics]{plot.default}}.
#' @param Tags List of tags to specify which episodes, as
#' apnoea or oxygen desaturation, are included in the plot.
#' \emph{Tags}="all" plots all episodes present in the data.
#' @param Indexes List of indexes of episodes (see \code{\link{ListEpisodes}})
#' to specify which episodes are included in the plot.
#' \emph{Indexes}="all" plots all episodes present in the data.
#' @param Tag Deprecated argument maintained for
#' compatibility, use Tags instead
#' @param eplim Two-component vector specifying the y-range (min,max) for the
#' vertical lines limiting each episode.
#' @param epColorPalette Vector specifying the color of each of the episodes that
#' will be plotted. The length of colorPalette should be equal or greater than
#' the number of different episodes to be plotted.
#' @param markEpisodes Boolean specyfing if a horizontal mark should be included
#' for each of the episodes.
#' @param ymark Two-component vector specifying the y-range (min,max) for the
#' horizontal marks. Only used if markEpisodes = TRUE.
#' @param showEpLegend Boolean argument. If TRUE, a legend of the episodes is
#' included.
#' @param epLegendCoords Two-component vector specifiying the coordinates where
#' the legend should be placed. By defaul, the legend is placed on top of the
#' plot.
#' @param ... Other graphical parameters for plotting the power band. See
#' \code{\link[graphics]{plot.default}}.
#' @seealso \code{\link{CalculatePowerBand}} for power calculation
#' @examples
#' \dontrun{
#'
#' # Read file "a03" from the physionet apnea-ecg database
#' library(RHRV)
#' HRVData <- CreateHRVData()
#' HRVData <- LoadBeatWFDB(HRVData,RecordName="test_files/WFDB/a03")
#' HRVData <- LoadApneaWFDB(HRVData,RecordName="test_files/WFDB/a03")
#' # Calculating heart rate signal:
#' HRVData <- BuildNIHR(HRVData)
#'
#' # Filtering heart rate signal:
#' HRVData <- FilterNIHR(HRVData)
#'
#' # Interpolating heart rate signal:
#' HRVData = InterpolateNIHR(HRVData)
#'
#' HRVData = CreateFreqAnalysis(HRVData)
#' HRVData = CalculatePowerBand(HRVData, indexFreqAnalysis = 1,
#' size = 300, shift = 60, sizesp = 1024)
#'
#' layout(matrix(1:4, nrow = 2))
#' PlotSinglePowerBand(HRVData, 1, "VLF", Tags = "APNEA", epColorPalette = "red",
#' epLegendCoords = c(2000,7500))
#' PlotSinglePowerBand(HRVData, 1, "LF", Tags = "APNEA", epColorPalette = "red",
#' eplim = c(0,6000),
#' markEpisodes = F, showEpLegend = FALSE)
#' PlotSinglePowerBand(HRVData, 1, "HF", Tags = "APNEA", epColorPalette = "red",
#' epLegendCoords = c(2000,1700))
#' PlotSinglePowerBand(HRVData, 1, "LF/HF", Tags = "APNEA", epColorPalette = "red",
#' eplim = c(0,20),
#' markEpisodes = F, showEpLegend = FALSE)
#' # Reset layout
#' par(mfrow = c(1,1))
#' }
PlotSinglePowerBand <-
function(HRVData, indexFreqAnalysis = length(HRVData$FreqAnalysis),
band = c("LF","HF","ULF","VLF","LF/HF"),
normalized = FALSE, main = paste(band, "Power Band"), xlab ="Time",
ylab = paste("Power in", band), type = "l",
Tags = NULL, Indexes = NULL,
eplim = NULL, epColorPalette = NULL,
markEpisodes = TRUE, ymark = NULL,
showEpLegend = TRUE, epLegendCoords = NULL, Tag = NULL,
...){
CheckAnalysisIndex(indexFreqAnalysis, length(HRVData$FreqAnalysis),
"frequency")
CheckPowerBand(HRVData, indexFreqAnalysis)
Tags = HandleDeprecatedTagArgument(Tag = Tag, Tags = Tags)
Tags = CheckTags(Tags, HRVData$Episodes)
Indexes = CheckIndexes(Indexes, HRVData$Episodes)
band = match.arg(band)
if (band == "LF/HF") {
band = "LFHF"
}
VerboseMessage(HRVData$Verbose, "Plotting power per band")
bandData = HRVData$FreqAnalysis[[indexFreqAnalysis]][[band]]
if (normalized) {
bandData = bandData / (max(bandData) - min(bandData))
VerboseMessage(HRVData$Verbose, "Power per band normalized")
}
timeAxis = HRVData$FreqAnalysis[[indexFreqAnalysis]]$Time
plot(timeAxis, bandData, main = main, xlab = xlab,
ylab = ylab, type = type, ... )
# Episodes plotting
if (!is.null(Tags) || !is.null(Indexes)) {
ylim = list(...)$ylim
if (is.null(ylim)) ylim = range(bandData, finite = TRUE)
if (is.null(eplim)) eplim = c(ylim[1], 0.90 * ylim[2])
if (is.null(ymark)) ymark = c(0.99 * eplim[2], eplim[2])
OverplotEpisodes(HRVData, Tags=Tags, Indexes=Indexes, eplim = eplim,
showEpLegend = showEpLegend,
epLegendCoords = epLegendCoords,
epColorPalette = epColorPalette,
markEpisodes = markEpisodes,
ymark = ymark)
}
}
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Defines functions PlotSinglePowerBand PlotPowerBand
Documented in PlotPowerBand PlotSinglePowerBand
#' PlotPowerBand
#' @title Plots power determined by CalculatePowerBand function
#' @description Plots the power of the heart rate signal at different bands
#' of physiological interest.
#' @param HRVData Data structure that stores the beats register and
#' information related to it
#' @param indexFreqAnalysis Numeric parameter used to reference a particular
#' frequency analysis
#' @param normalized Plots normalized powers if TRUE
#' @param hr Plots heart rate signal if TRUE
#' @param ymax Maximum value for y axis (unnormalized plots)
#' @param ymaxratio Maximum value for y axis in LF/HF band (normalized and
#' unnormalized plots)
#' @param ymaxnorm Maximum value for y axis (normalized plots)
#' @param Tags List of tags to specify which episodes, as apnoea or oxygen
#' desaturation, are included in the plot. Tags = "all" plots all episodes present
#' in the data.
#' @param Indexes List of indexes to specify which episodes (see ListEpisodes),
#' are included in the plot. Indexes = "all" plots all episodes present
#' in the data.
#' @param Tag Deprecated argument, use Tags instead
#' @param verbose Deprecated argument maintained for compatibility, use
#' setVerbose() instead
#' @references
#' L. Rodriguez-Linares, L., A.J. Mendez, M.J. Lado, D.N. Olivieri,
#' X.A. Vila, and I. Gomez-Conde, "An open source tool for heart rate
#' variability spectral analysis", Computer Methods and Programs in
#' Biomedicine 103(1):39-50, july 2011.
#' @author M. Lado, A. Mendez, D. Olivieri, L. Rodriguez, X. Vila
#' @note See \code{\link{PlotSinglePowerBand}} for a more flexible
#' function for plotting power bands.
#' @seealso \code{\link{CalculatePowerBand}} for power calculation
#' and \code{\link{PlotSinglePowerBand}}
#' @examples
#' \dontrun{
#' # Reading a wfdb register and storing into a data structure:
#' md = CreateHRVData(Verbose = TRUE)
#' md = LoadBeatWFDB(md, RecordName = "register_name",
#' RecordPath = "register_path")
#'
#' # Calculating heart rate signal:md = BuildNIHR(md)
#'
#' # Filtering heart rate signal:
#' md = FilterNIHR(md)
#' # Interpolating heart rate signal:
#' md = InterpolateNIHR(md)
#' # Calculating spectrogram and power per band:
#' md = CreateFreqAnalysis(md)
#' md = CalculatePowerBand(md, indexFreqAnalysis = 1, size = 120,
#' shift = 10, sizesp = 1024)
#' # Plotting Power per Band
#' PlotPowerBand(md, hr = TRUE, ymax = 700000, ymaxratio = 4)
#' }
#' @keywords hplot
PlotPowerBand <-
function(HRVData, indexFreqAnalysis = length(HRVData$FreqAnalysis),
normalized = FALSE, hr = FALSE, ymax = NULL, ymaxratio = NULL,
ymaxnorm = 1, Tags=NULL, Indexes=NULL, Tag = NULL, verbose = NULL) {
# --------------------
# Plots power per band
# --------------------
# indexFreqAnalysis: index of an existing frequency analysis to use
# normalized: plots normalized powers if TRUE
# hr: plots heart rate signal if TRUE
# ymax: maximum value for y axis (unnormalized plots)
# ymaxratio: maximum value for y axis in LF/HF band (normalized and unnormalized plots)
# Tags -> Tags of episodes to include in the plot
# "all" includes all types
# Indexes -> Indexes of episodes to include in the plot
# "all" includes all episodes
HRVData = HandleVerboseArgument(HRVData, verbose)
Tags = HandleDeprecatedTagArgument(Tag = Tag, Tags = Tags)
CheckAnalysisIndex(indexFreqAnalysis, length(HRVData$FreqAnalysis),
"frequency")
Tags = CheckTags(Tags, HRVData$Episodes)
Indexes = CheckIndexes(Indexes, HRVData$Episodes)
CheckPowerBand(HRVData, indexFreqAnalysis)
VerboseMessage(HRVData$Verbose,
"Plotting power per band")
# if (is.null(ymax)) {
# ymax = max(max(HRVData$FreqAnalysis[[indexFreqAnalysis]]$ULF) , max(HRVData$FreqAnalysis[[indexFreqAnalysis]]$VLF) , max(HRVData$FreqAnalysis[[indexFreqAnalysis]]$LF) , max(HRVData$FreqAnalysis[[indexFreqAnalysis]]$HF) )
# }
# normalization
if (normalized) {
HRVData$FreqAnalysis[[indexFreqAnalysis]]$ULF=(HRVData$FreqAnalysis[[indexFreqAnalysis]]$ULF-min(HRVData$FreqAnalysis[[indexFreqAnalysis]]$ULF))/(max(HRVData$FreqAnalysis[[indexFreqAnalysis]]$ULF)-min(HRVData$FreqAnalysis[[indexFreqAnalysis]]$ULF))
HRVData$FreqAnalysis[[indexFreqAnalysis]]$VLF=(HRVData$FreqAnalysis[[indexFreqAnalysis]]$VLF-min(HRVData$FreqAnalysis[[indexFreqAnalysis]]$VLF))/(max(HRVData$FreqAnalysis[[indexFreqAnalysis]]$VLF)-min(HRVData$FreqAnalysis[[indexFreqAnalysis]]$VLF))
HRVData$FreqAnalysis[[indexFreqAnalysis]]$LF=(HRVData$FreqAnalysis[[indexFreqAnalysis]]$LF-min(HRVData$FreqAnalysis[[indexFreqAnalysis]]$LF))/(max(HRVData$FreqAnalysis[[indexFreqAnalysis]]$LF)-min(HRVData$FreqAnalysis[[indexFreqAnalysis]]$LF))
HRVData$FreqAnalysis[[indexFreqAnalysis]]$HF=(HRVData$FreqAnalysis[[indexFreqAnalysis]]$HF-min(HRVData$FreqAnalysis[[indexFreqAnalysis]]$HF))/(max(HRVData$FreqAnalysis[[indexFreqAnalysis]]$HF)-min(HRVData$FreqAnalysis[[indexFreqAnalysis]]$HF))
# HRVData$FreqAnalysis[[indexFreqAnalysis]]$LFHF=(HRVData$FreqAnalysis[[indexFreqAnalysis]]$LFHF-min(HRVData$FreqAnalysis[[indexFreqAnalysis]]$LFHF))/(max(HRVData$FreqAnalysis[[indexFreqAnalysis]]$LFHF)-min(HRVData$FreqAnalysis[[indexFreqAnalysis]]$LFHF))
VerboseMessage(HRVData$Verbose,
"Power per band normalized")
}
if (hr)
numfilas=6
else
numfilas=5
# lframes is the number of frames for plotting power per band
lframes=length(HRVData$FreqAnalysis[[indexFreqAnalysis]]$HRV)
timeAxis = HRVData$FreqAnalysis[[indexFreqAnalysis]]$Time
# Episodes
if (!is.null(Tags) || !is.null(Indexes)) {
EpisodesToPlot <- selectEpisodes(HRVData$Episodes,Tags,Indexes)
EpisodesToPlot <- EpisodesToPlot[EpisodesToPlot$selected,]
# Data for representing episodes
EpisodesAuxLeft=EpisodesToPlot$InitTime
# EpisodesAuxLeftFrame=EpisodesAuxLeft*lframes/(tail(HRVData$Beat$Time,1)-head(HRVData$Beat$Time,1)) # Beg of episodes (frames)
EpisodesAuxRight=EpisodesToPlot$InitTime + EpisodesToPlot$Duration
# EpisodesAuxRightFrame=EpisodesAuxRight*lframes/(tail(HRVData$Beat$Time,1)-head(HRVData$Beat$Time,1)) # Beg of episodes (frames)
EpisodesAuxType=EpisodesToPlot$Type
VerboseMessage(HRVData$Verbose,
paste("No of episodes:", length(EpisodesAuxLeft)))
labels <- levels(factor(EpisodesAuxType))
Pal=rainbow(length(labels))
Bor=Pal[match(EpisodesAuxType,labels)]
EpisodesLeft=HRVData$Episodes$InitTime # Beg of episodes (seconds)
#EpisodesLeftFrame=EpisodesLeft*lframes/(tail(HRVData$Beat$Time,1)-head(HRVData$Beat$Time,1)) # Beg of episodes (frames)
EpisodesRight=HRVData$Episodes$InitTime+HRVData$Episodes$Duration # Beg of episodes (seconds)
#EpisodesRightFrame=EpisodesRight*lframes/(tail(HRVData$Beat$Time,1)-head(HRVData$Beat$Time,1)) # Beg of episodes (frames)
}
previousPar = par()
par(mfrow=c(numfilas,1),omi=c(0,0,0,0),
mai=c(0,0,0,0),mar=c(3,4,1,1),
oma=c(1,0,2,0),mgp=c(1.5,.5,0))
#on.exit(par(previousPar))
# ---------- LF/HF ----------
if (is.null(ymaxratio)) {
ymaxratio = max(HRVData$FreqAnalysis[[indexFreqAnalysis]]$LFHF)
}
mfg=c(1,1,numfilas,1)
plot(timeAxis,HRVData$FreqAnalysis[[indexFreqAnalysis]]$LFHF,
type='l',xlab="",ylab="LF/HF",ylim=c(0,ymaxratio*1.1))
if (!is.null(Tags) || !is.null(Indexes)) {
EpisodesAuxTop=c(ymaxratio*1.09,ymaxratio*1.04)
EpisodesAuxBottom=c(ymaxratio*1.06,ymaxratio*1.01)
rect(EpisodesAuxLeft,EpisodesAuxBottom,
EpisodesAuxRight,EpisodesAuxTop,
border=Bor,col=Bor)
for (i in 1:length(EpisodesAuxLeft)) {
lines(rep(EpisodesAuxLeft[i],times=2),
c(0,ymaxratio*1.1),lty=2,col=Bor[i])
lines(rep(EpisodesAuxRight[i],times=2),
c(0,ymaxratio*1.1),lty=2,col=Bor[i])
}
par(xpd=NA)
legend(timeAxis[lframes/2],ymaxratio,
legend=Tags,fill=Pal,cex=0.9,ncol=length(Tags),
xjust=0.5,yjust=-0.2,bty="n")
}
VerboseMessage(HRVData$Verbose,
"Plotted LF/HF")
# ---------- ULF ----------
if (normalized==TRUE) {
ymaxv=c(0,ymaxnorm)
} else if (!is.null(ymax)) {
ymaxv=c(0,ymax)
} else {
ymaxv = c(0,max(HRVData$FreqAnalysis[[indexFreqAnalysis]]$ULF))
}
mfg=c(1,2,numfilas,1)
plot(timeAxis,
HRVData$FreqAnalysis[[indexFreqAnalysis]]$ULF,
type='l',xlab="",ylab="ULF",ylim=ymaxv)
if (!is.null(Tags) || !is.null(Indexes)) {
for (i in 1:length(EpisodesAuxLeft)) {
lines(rep(EpisodesAuxLeft[i],times=2),
c(ymaxv[1],ymaxv[2]),lty=2,col=Bor[i])
lines(rep(EpisodesAuxRight[i],times=2),
c(ymaxv[1],ymaxv[2]),lty=2,col=Bor[i])
}
}
VerboseMessage(HRVData$Verbose, "Plotted ULF")
# ---------- VLF ----------
if (normalized==TRUE) {
ymaxv=c(0,ymaxnorm)
} else if (!is.null(ymax)) {
ymaxv=c(0,ymax)
} else {
ymaxv = c(0,max(HRVData$FreqAnalysis[[indexFreqAnalysis]]$VLF))
}
mfg=c(1,3,numfilas,1)
plot(timeAxis,
HRVData$FreqAnalysis[[indexFreqAnalysis]]$VLF,
type='l',xlab="",ylab="VLF",ylim=ymaxv)
if (!is.null(Tags) || !is.null(Indexes)) {
for (i in 1:length(EpisodesAuxLeft)) {
lines(rep(EpisodesAuxLeft[i],times=2),
c(ymaxv[1],ymaxv[2]),lty=2,col=Bor[i])
lines(rep(EpisodesAuxRight[i],times=2),
c(ymaxv[1],ymaxv[2]),lty=2,col=Bor[i])
}
}
VerboseMessage(HRVData$Verbose, "Plotted VLF")
# ---------- LF ----------
if (normalized==TRUE) {
ymaxv=c(0,ymaxnorm)
} else if (!is.null(ymax)) {
ymaxv=c(0,ymax)
} else {
ymaxv = c(0,max(HRVData$FreqAnalysis[[indexFreqAnalysis]]$LF))
}
mfg=c(1,4,numfilas,1)
plot(timeAxis,
HRVData$FreqAnalysis[[indexFreqAnalysis]]$LF,type='l',xlab="",ylab="LF",ylim=ymaxv)
if (!is.null(Tags) || !is.null(Indexes)) {
for (i in 1:length(EpisodesAuxLeft)) {
lines(rep(EpisodesAuxLeft[i],times=2),
c(ymaxv[1],ymaxv[2]),lty=2,col=Bor[i])
lines(rep(EpisodesAuxRight[i],times=2),
c(ymaxv[1],ymaxv[2]),lty=2,col=Bor[i])
}
}
VerboseMessage(HRVData$Verbose, "Plotted LF")
# ---------- HF ----------
if (normalized==TRUE) {
ymaxv=c(0,ymaxnorm)
} else if (!is.null(ymax)) {
ymaxv=c(0,ymax)
} else {
ymaxv = c(0,max(HRVData$FreqAnalysis[[indexFreqAnalysis]]$HF))
}
mfg=c(1,5,numfilas,1)
texto4="Time (seconds)"
plot(timeAxis,
HRVData$FreqAnalysis[[indexFreqAnalysis]]$HF,type='l',xlab=texto4,ylab="HF",ylim=ymaxv)
if (!is.null(Tags) || !is.null(Indexes)) {
for (i in 1:length(EpisodesAuxLeft)) {
lines(rep(EpisodesAuxLeft[i],times=2),
c(ymaxv[1],ymaxv[2]),lty=2,col=Bor[i])
lines(rep(EpisodesAuxRight[i],times=2),
c(ymaxv[1],ymaxv[2]),lty=2,col=Bor[i])
}
}
VerboseMessage(HRVData$Verbose, "Plotted HF")
# ---------- HR ----------
if (numfilas==6) {
mfg=c(1,6,numfilas,1)
# lsecs is the duration of the record in seconds for plotting heart rate signal
lsecs=tail(HRVData$Beat$Time,1)-head(HRVData$Beat$Time,1)
plot(seq(head(HRVData$Beat$Time,1),tail(HRVData$Beat$Time,1),by=1/HRVData$Freq_HR),
HRVData$HR,type='l',xlab="Time (sec.)",ylab="HR (bps)")
VerboseMessage(HRVData$Verbose,"Plotted HRV")
if (!is.null(Tags) || !is.null(Indexes)) {
for (i in 1:length(EpisodesAuxLeft)) {
lines(rep(EpisodesAuxLeft[i],times=2),
c(min(HRVData$HR),max(HRVData$HR)),lty=2,col=Bor[i])
lines(rep(EpisodesAuxRight[i],times=2),
c(min(HRVData$HR),max(HRVData$HR)),lty=2,col=Bor[i])
}
#rect(EpisodesAuxLeft,rep(min(HRVData$HR),times=length(EpisodesAuxLeft)),EpisodesAuxRight,rep(max(HRVData$HR),times=length(EpisodesAuxLeft)),border=Bor)
}
# --------------------
}
if ( !is.null(Tags) || !is.null(Indexes) ) {
VerboseMessage(HRVData$Verbose, "Episodes plotted")
}
if ((normalized == TRUE) && (numfilas == 6))
title(main="Normalized power bands of HRV and Heart Rate Signal",outer=TRUE)
else if ((normalized == FALSE) && (numfilas == 6))
title(main="Power bands of HRV and Heart Rate Signal",outer=TRUE)
else if ((normalized == TRUE) && (numfilas != 6))
title(main="Normalized power bands of HRV",outer=TRUE)
else
title(main="Power bands of HRV",outer=TRUE)
VerboseMessage(HRVData$Verbose, "Power per band plotted")
#restore previous graphical parameters
par(mfrow=previousPar$mfrow, omi=previousPar$omi, mai=previousPar$mai,
mar=previousPar$mar,oma=previousPar$oma,mgp=previousPar$mgp)
}
#' PlotSinglePowerBand
#' @description Plots a concrete power band computed by the CalculatePowerBand
#' function
#' @param HRVData Data structure that stores the beats register and
#' information related to it
#' @param indexFreqAnalysis Numeric parameter used to reference a particular
#' frequency analysis
#' @param band The frequency band to be plotted. Allowd bands are "ULF", "VLF", "LF"
#' (default), "HF" and "LF/HF")
#' @param normalized Plots normalized powers if TRUE
#' @param main A main title for the plot.
#' @param xlab A label for the x axis.
#' @param ylab A label for the y axis
#' @param type 1-character string giving the type of plot desired. See
#' \code{\link[graphics]{plot.default}}.
#' @param Tags List of tags to specify which episodes, as
#' apnoea or oxygen desaturation, are included in the plot.
#' \emph{Tags}="all" plots all episodes present in the data.
#' @param Indexes List of indexes of episodes (see \code{\link{ListEpisodes}})
#' to specify which episodes are included in the plot.
#' \emph{Indexes}="all" plots all episodes present in the data.
#' @param Tag Deprecated argument maintained for
#' compatibility, use Tags instead
#' @param eplim Two-component vector specifying the y-range (min,max) for the
#' vertical lines limiting each episode.
#' @param epColorPalette Vector specifying the color of each of the episodes that
#' will be plotted. The length of colorPalette should be equal or greater than
#' the number of different episodes to be plotted.
#' @param markEpisodes Boolean specyfing if a horizontal mark should be included
#' for each of the episodes.
#' @param ymark Two-component vector specifying the y-range (min,max) for the
#' horizontal marks. Only used if markEpisodes = TRUE.
#' @param showEpLegend Boolean argument. If TRUE, a legend of the episodes is
#' included.
#' @param epLegendCoords Two-component vector specifiying the coordinates where
#' the legend should be placed. By defaul, the legend is placed on top of the
#' plot.
#' @param ... Other graphical parameters for plotting the power band. See
#' \code{\link[graphics]{plot.default}}.
#' @seealso \code{\link{CalculatePowerBand}} for power calculation
#' @examples
#' \dontrun{
#'
#' # Read file "a03" from the physionet apnea-ecg database
#' library(RHRV)
#' HRVData <- CreateHRVData()
#' HRVData <- LoadBeatWFDB(HRVData,RecordName="test_files/WFDB/a03")
#' HRVData <- LoadApneaWFDB(HRVData,RecordName="test_files/WFDB/a03")
#' # Calculating heart rate signal:
#' HRVData <- BuildNIHR(HRVData)
#'
#' # Filtering heart rate signal:
#' HRVData <- FilterNIHR(HRVData)
#'
#' # Interpolating heart rate signal:
#' HRVData = InterpolateNIHR(HRVData)
#'
#' HRVData = CreateFreqAnalysis(HRVData)
#' HRVData = CalculatePowerBand(HRVData, indexFreqAnalysis = 1,
#' size = 300, shift = 60, sizesp = 1024)
#'
#' layout(matrix(1:4, nrow = 2))
#' PlotSinglePowerBand(HRVData, 1, "VLF", Tags = "APNEA", epColorPalette = "red",
#' epLegendCoords = c(2000,7500))
#' PlotSinglePowerBand(HRVData, 1, "LF", Tags = "APNEA", epColorPalette = "red",
#' eplim = c(0,6000),
#' markEpisodes = F, showEpLegend = FALSE)
#' PlotSinglePowerBand(HRVData, 1, "HF", Tags = "APNEA", epColorPalette = "red",
#' epLegendCoords = c(2000,1700))
#' PlotSinglePowerBand(HRVData, 1, "LF/HF", Tags = "APNEA", epColorPalette = "red",
#' eplim = c(0,20),
#' markEpisodes = F, showEpLegend = FALSE)
#' # Reset layout
#' par(mfrow = c(1,1))
#' }
PlotSinglePowerBand <-
function(HRVData, indexFreqAnalysis = length(HRVData$FreqAnalysis),
band = c("LF","HF","ULF","VLF","LF/HF"),
normalized = FALSE, main = paste(band, "Power Band"), xlab ="Time",
ylab = paste("Power in", band), type = "l",
Tags = NULL, Indexes = NULL,
eplim = NULL, epColorPalette = NULL,
markEpisodes = TRUE, ymark = NULL,
showEpLegend = TRUE, epLegendCoords = NULL, Tag = NULL,
...){
CheckAnalysisIndex(indexFreqAnalysis, length(HRVData$FreqAnalysis),
"frequency")
CheckPowerBand(HRVData, indexFreqAnalysis)
Tags = HandleDeprecatedTagArgument(Tag = Tag, Tags = Tags)
Tags = CheckTags(Tags, HRVData$Episodes)
Indexes = CheckIndexes(Indexes, HRVData$Episodes)
band = match.arg(band)
if (band == "LF/HF") {
band = "LFHF"
}
VerboseMessage(HRVData$Verbose, "Plotting power per band")
bandData = HRVData$FreqAnalysis[[indexFreqAnalysis]][[band]]
if (normalized) {
bandData = bandData / (max(bandData) - min(bandData))
VerboseMessage(HRVData$Verbose, "Power per band normalized")
}
timeAxis = HRVData$FreqAnalysis[[indexFreqAnalysis]]$Time
plot(timeAxis, bandData, main = main, xlab = xlab,
ylab = ylab, type = type, ... )
# Episodes plotting
if (!is.null(Tags) || !is.null(Indexes)) {
ylim = list(...)$ylim
if (is.null(ylim)) ylim = range(bandData, finite = TRUE)
if (is.null(eplim)) eplim = c(ylim[1], 0.90 * ylim[2])
if (is.null(ymark)) ymark = c(0.99 * eplim[2], eplim[2])
OverplotEpisodes(HRVData, Tags=Tags, Indexes=Indexes, eplim = eplim,
showEpLegend = showEpLegend,
epLegendCoords = epLegendCoords,
epColorPalette = epColorPalette,
markEpisodes = markEpisodes,
ymark = ymark)
}
}
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