MAplot function

Minus versus Add plot

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

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 eitherClassplot 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.

Returns

• 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

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.

Author(s)

Michael Thrun

Examples

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