Usage
"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
called.pch
the symbol of points with false discovery rate, q
called.cex
the character expansion of points with false discovery rate, q
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