MAplot: Minus versus Add plot

In Mthrun/DataVisualizations: Visualizations of High-Dimensional Data

Minus versus Add plot

Description

Bland-Altman plot [Altman/Bland, 1983].

Usage

MAplot(X,Y,islog=TRUE,LoA=FALSE,CI=FALSE,

densityplot=FALSE,main,xlab,ylab,

Cls,lwd=2,ylim=NULL,...)

Arguments

X	[1:n] numerical vector of a feature/variable
Y	[1:n] another numerical vector of a feature/variable
islog	Optional, TRUE: MAplot, FALSE: M=x-y versus a=0.5(x+y)
LoA	Optional, if TRUE: limits of agreement are plottet as lines if densityplot=FALSE
CI	Optional, if TRUE: confidence intervals for LoA, see [Stockl et al., 2004], if densityplot=FALSE
densityplot	Optional, FALSE: Scatterplot using Classplot, TRUE: density scatter plot with DensityScatter
main	Optional, see plot
xlab	Optional, see plot
ylab	Optional, see plot
Cls	Optional, prior Classification as a numeric vector.
lwd	Optional, if LoA=TRUE or CI=TRUE the width of the lines, otherwise input argument is ignored
ylim	Optional, default =NULL sets this parameter automatically, otherwise see Classplot.
...	for example, ylim, Please see either Classplot in the mode Plotter="native", or DensityScatter for further arguments depending on densityplot, see also details

Details

Bland-Altman plot [Altman/Bland, 1983] for visual representation of genomic data or in order to decorrelate data.

"The limits of agreement (LoA) are defined as the mean difference +- 1.96 SD of differences. If these limits do not exceed the maximum allowed difference between methods (the differences within mean +- 1.96 SD are not clinically important), the two methods are considered to be in agreement and may be used interchangeably." cited as in URL. Please note, that the underyling assumption is the normal distribution of the differences. Input argument LoA=TRUE shows the mean of the difference in blue and +- 1.96 SD in green. Input argument CI=TRUE shows the mean of the difference in blue and the confidence intervall as red dashed lines similar to the cited URL.

In case of densityplot=FALSE, the function Classplot is always called with Plotter="native". Then, the input argument "Colors"" of points can only be set in Classplot if "Cls"" is given in this function, otherwise the points are always black. The input argument "Size"" sets the size of points in Classplot.

Value

MA	[1:n,2] Matrix of Minus component of two features and Add component of two features
Handle	see DensityScatter for output options, if densityplot=TRUE, otherwise NULL
Statistics	Named list of four element, each consisting of one value depending on input parameters LoA and CI, of this function. If not specifically set each list element is NULL. The elements are Mean_value - mean allowed difference, SD_value - standard deviation of difference, LoA_value - Limits of agreement=1.96*SD, CI_value - confidence intervall, i.e., maximum allowed difference

Author(s)

Michael Thrun

References

[Altman/Bland, 1983] Altman D.G., Bland J.M.: Measurement in medicine: the analysis of method comparison studies, The Statistician, Vol. 32, p. 307-317, doi:10.2307/2987937, 1983.

https://www.medcalc.org/manual/bland-altman-plot.php

[Stockl et al., 2004] Stockl, D., Rodriguez Cabaleiro, D., Van Uytfanghe, K., & Thienpont, L. M.: Interpreting method comparison studies by use of the Bland-Altman plot: reflecting the importance of sample size by incorporating confidence limits and predefined error limits in the graphic, Clinical chemistry, Vol. 50(11), pp. 2216-2218. 2004.

Examples

data("ITS")
data("MTY")
MAlist=MAplot(ITS,MTY)

Mthrun/DataVisualizations documentation built on Jan. 16, 2024, 1:01 a.m.