Plot an aldex Object

Description

Create ‘MW’- or ‘MA’-type plots from the given aldex object.

Usage

1
2
3
4
5
6
7
8
    ## S3 method for class 'plot'
aldex(  x, ..., type=c("MW","MA"),
    xlab=NULL, ylab=NULL, xlim=NULL, ylim=NULL,
    all.col=rgb(0,0,0,0.2), all.pch=19, all.cex=0.4,
    called.col=red, called.pch=20, called.cex=0.6,
    thres.line.col=darkgrey, thres.lwd=1.5,
    test=welch, cutoff=0.1, rare.col=black, rare=0,
    rare.pch=20, rare.cex=0.2 )

Arguments

x

an object of class aldex produced by the aldex function

...

optional, unused arguments included for compatibility withe the S3 method signature

type

which type of plot is to be produced. MA is a Bland-Altman style plot; MW is a difference between to a variance within plot as described in the paper

test

the method of calculating significance, one of: welch = welch's t test; wilcox = wilcox rank test; glm = glm; kruskal = Kruskal-Wallace test

cutoff

the Benjamini-Hochberg fdr cutoff, default 0.1

xlab

the x-label for the plot, as per the parent plot function

ylab

the y-label for the plot, as per the parent plot function

xlim

the x-limits for the plot, as per the parent plot function

ylim

the y-limits for the plot, as per the parent plot function

all.col

the default colour of the plotted points

all.pch

the default plotting symbol

all.cex

the default symbol size

called.col

the colour of points with false discovery rate, q <= 0.1

called.pch

the symbol of points with false discovery rate, q <= 0.1

called.cex

the character expansion of points with false discovery rate, q <= 0.1

thres.line.col

the colour of the threshold line where within and between group variation is equivalent

thres.lwd

the width of the threshold line where within and between group variation is equivalent

rare

relative abundance cutoff for rare features, default 0 or the mean abundance

rare.col

color for rare features, default black

rare.pch

the default symbol of rare features

rare.cex

the default symbol size of rare points

Details

This particular specialization of the plot function is relatively simple and provided for convenience. For more advanced control of the plot is is best to use the values returned by summary(x).

Value

None.

References

Please use the citation given by citation(package="ALDEx").

See Also

aldex, aldex.effect, aldex.ttest, aldex.glm

Examples

1
    # See the examples for 'aldex'.