plotClassTimeSeries: Plot abundances by class

In HCBravoLab/metagenomeSeq: Statistical analysis for sparse high-throughput sequencing

Plot abundances by class

Description

Plot the abundance of values for each class using a spline approach on the estimated full model.

Usage

plotClassTimeSeries(
  res,
  formula,
  xlab = "Time",
  ylab = "Abundance",
  color0 = "black",
  color1 = "red",
  include = c("1", "class", "time:class"),
  ...
)

Arguments

res	Output of fitTimeSeries function
formula	Formula for ssanova. Of the form: abundance ~ ... where ... includes any pData slot value.
xlab	X-label.
ylab	Y-label.
color0	Color of samples from first group.
color1	Color of samples from second group.
include	Parameters to include in prediction.
...	Extra plotting arguments.

Value

Plot for abundances of each class using a spline approach on estimated null model.

See Also

fitTimeSeries

Examples

data(mouseData)
res = fitTimeSeries(obj=mouseData,feature="Actinobacteria",
   class="status",id="mouseID",time="relativeTime",lvl='class',B=10)
plotClassTimeSeries(res,pch=21,bg=res$data$class,ylim=c(0,8))

HCBravoLab/metagenomeSeq documentation built on March 17, 2024, 3:21 p.m.