drawBW: BW and percentile ratios plot

In speaq: Tools for Nuclear Magnetic Resonance (NMR) Spectra Alignment, Peak Based Processing, Quantitative Analysis and Visualizations

BW and percentile ratios plot

Description

This function is used to plot BW and percentile ratios

Usage

drawBW(
  BW,
  perc,
  X,
  startP = -1,
  endP = -1,
  groupLabel = NULL,
  highBound = -1,
  lowBound = -1,
  nAxisPos = 4,
  offside = 0
)

Arguments

BW	An array of the BW ratios.
perc	An array of the percentile ratios.
X	The spectral dataset in matrix format in which each row contains a single sample.
startP	The starting point of the segment. If it is -1, the starting point is from beginning of the spectra.
endP	The ending point of the segment. If it is -1, the ending point is the last point of the spectra.
groupLabel	The default value is NULL, it means that a single spectrum has a distinct color. Otherwise, the spectra is colored by their label.
highBound	Default value is -1, that means the plot covers also the highest intensity peaks in the figure. If the users want to limit the upper height of the figure, set this parameter by the limited value.
lowBound	Default value is -1, that means the plot covers also the lowest intensity peaks in the figure. If the users want to limit the under height of the figure, set this parameter by the limited value.
nAxisPos	The number of ticks that will be displayed in the horizontal axis.
offside	The offside of values in x-axis for display.

Value

Return a plot containing both the BW and the spectra.

Author(s)

Trung Nghia Vu

See Also

drawSpec

Examples

res=makeSimulatedData();
X=res$data;
groupLabel=res$label;
peakList <- detectSpecPeaks(X,
                            nDivRange = c(128),
                            scales = seq(1, 16, 2),
                            baselineThresh = 50000,
                            SNR.Th = -1,
                            verbose=FALSE
);
resFindRef<- findRef(peakList);
refInd <- resFindRef$refInd;
maxShift = 50;
Y <- dohCluster(X,
                peakList = peakList,
                refInd = refInd,
                maxShift  = maxShift,
                acceptLostPeak = TRUE, verbose=FALSE);
# find the BW-statistic
BW = BWR(Y, groupLabel);
N = 100;
alpha = 0.05;
# create sampled H0 and export to file
H0 = createNullSampling(Y, groupLabel, N = N,verbose=FALSE)
#compute percentile of alpha
perc = double(ncol(Y));
alpha_corr = alpha/sum(returnLocalMaxima(Y[2,])$pkMax>50000);
for (i in seq_along(perc)) {
    perc[i] = quantile(H0[,i],1-alpha_corr, type = 3);
}
drawBW(BW, perc,Y, groupLabel = groupLabel)

speaq documentation built on May 23, 2022, 5:06 p.m.