aldex.glm.plot: Plot an 'aldex' Object

In ggloor/ALDEx_bioc: Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account

Plot an aldex Object

Description

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

Usage

aldex.glm.plot(
  x,
  ...,
  eff = NULL,
  contrast = NULL,
  test = "fdr",
  type = c("MW", "MA", "volcano"),
  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,
  cutoff.pval = 0.05,
  cutoff.effect = 1,
  rare.col = "black",
  rare = 0,
  rare.pch = 20,
  rare.cex = 0.2
)

Arguments

x	an object produced by the aldex.glm function
...	optional, unused arguments included for compatibility with the S3 method signature
eff	an object produced by the aldex.glm.effect function
contrast	the column name of the model matrix contrast to plot
test	the method of calculating significance, one of "pval" or "fdr"
type	which type of plot is to be produced. MA is a Bland-Altman style plot; MW is an effect plot showing the relationship of difference between and dispersion as described in: http://dx.doi.org/10.1080/10618600.2015.1131161; volcano is a volcano plot http://dx.doi.org/10.1186/gb-2003-4-4-210
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 <= 0.05
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
cutoff.pval	the fdr cutoff, default 0.05
cutoff.effect	the effect size cutoff for plotting, default 1
rare.col	color for rare features, default black
rare	relative abundance cutoff for rare features, default 0 or the mean abundance
rare.pch	the default symbol of rare features
rare.cex	the default symbol size of rare points

Details

Plot an aldex Object

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.glm'

ggloor/ALDEx_bioc documentation built on Oct. 31, 2023, 1:13 a.m.