rpaplot: rpaplot Plot RPA results and probe-level data for a specified...

In microbiome/RPA: RPA: Robust Probabilistic Averaging for probe-level analysis

rpaplot Plot RPA results and probe-level data for a specified probeset.

Description

rpaplot Plot RPA results and probe-level data for a specified probeset.

Usage

rpaplot(
  dat,
  mu = NULL,
  tau2 = NULL,
  affinity = NULL,
  highlight.probes = NULL,
  pcol = "darkgrey",
  mucol = "black",
  ecol = "red",
  cex.lab = 1.5,
  cex.axis = 1,
  cex.main = 1,
  cex.names = 1,
  external.signal = NULL,
  main = "",
  plots = "all",
  ...
)

Arguments

dat	Background-corrected and normalized data: probes x samples.
mu	probeset signal
tau2	probe variances
affinity	probe affinities
highlight.probes	Optionally highlight some of the probes (with dashed line)
pcol	Color for probe signal visualization.
mucol	Color for summary estimate.
ecol	Color for external signal.
cex.lab	Label size adjustment parameters.
cex.axis	Axis size adjustment parameters.
cex.main	Title size adjustment parameters.
cex.names	Names size adjustment parameters.
external.signal	Plot external signal on the probeset. For instance, an alternative summary estimate from another preprocessing methods
main	Title text.
plots	"all": plot data and summary, noise and affinity; "data": plot data and summary
...	Other parameters to pass for plot function.

Details

Plots the preprocessed probe-level observations, estimated probeset-level signal, and probe-specific variances. It is also possible to highlight individual probes and external summary measures.

Value

Used for its side-effects. Returns probes x samples matrix of probe-level data plotted on the image.

Author(s)

Leo Lahti [e-mail]

References

See citation("RPA")

Examples

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microbiome/RPA documentation built on April 9, 2023, 10:59 a.m.