plot.aldex: Plot an 'aldex' Object
In ALDEx2: Analysis Of Differential Abundance Taking Sample Variation Into Account

Description Usage Arguments Details Value References See Also Examples

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

    ## 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.pval=0.1, cutoff.effect=1, rare.col=black,
    rare=0, rare.pch=20, rare.cex=0.2 )

`x`	an object of class `aldex` produced by the `aldex` function
`...`	optional, unused arguments included for compatibility with 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: http://dx.doi.org/10.1080/10618600.2015.1131161
`test`	the method of calculating significance, one of: welch = welch's t test; wilcox = wilcox rank test; glm = glm; kruskal = Kruskal-Wallace test
`cutoff.pval`	the Benjamini-Hochberg fdr cutoff, default 0.1
`cutoff.effect`	the effect size cutoff for plotting, default 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

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).

None.

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

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

1	# See the examples for 'aldex'.

Warning messages:
1: no function found corresponding to methods exports from 'DelayedArray' for: 'acbind', 'arbind' 
2: no function found corresponding to methods exports from 'SummarizedExperiment' for: 'acbind', 'arbind'