aldex.plot {ALDEx2} | R Documentation

## Plot an `aldex` Object

### Description

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

### Usage

        ## 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 )

### Arguments

`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

### 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

        # See the examples for 'aldex'.

[Package ALDEx2 version 1.20.0 Index]