plot.hisemit: Plot a hisemit object

Description

Plot an object of class hisemit

Usage

# S3 method for hisemit
plot(x, type = c("tuning", "residual"), ...)
plotHisemitResid(obj, y.type = c("hist", "scatter"), 
        x.type = c("lfdr", "pi0", "f"), ...)
plotHisemitTuning(obj, SE = FALSE, add = FALSE, ...)

Arguments

x,obj

The object of class hisemit

type

Either 'tuning' or 'residual', the type of plot requested.

…

See Details.

y.type

Either 'hist' or 'scatter', the type of residual plot requested.

x.type

One of 'lfdr', 'pi0' or 'f', the x-axis when y.type='scatter'.

A logical scalar, indicating whether standard error bars should be added to the plot.

add

A logical scaler, indicating whether a new plot should be generated or adding lines to the existing plot.

Value

For histograms of residuals, an object from hist is returned. For scatter plot of residuals, an object from plot is returned. For tuning plot, a matrix with the range of tuning criterion is returned.

Details

The generic function plot.hisemit calls either plotHisemitResid or plotHisemitTuning depending on type. For plot.hisemit, the … is the additinoal arguments to be passed to plotHisemitResid or plotHisemitTuning. For residual plot (plotHisemitResid), the … is the additional arguments to be passed to hist when y.type='hist'; and to residuals.hisemit when y.type='scatter'. For tuning plot (plotHisemitTuning), the … is the additional arguments to be passed to either plot or lines depending on add.

References

Long Qu, Dan Nettleton, Jack Dekkers (2012) A hierarchical semiparametric model for incorporating inter-gene relationship information for analysis of genomic data. Biometrics, 68(4):1168-1177