statgenHTP (version 1.0.8)

plot.singleOut: Plot outliers for single observations

Description

Plot the fitted local regression, confidence intervals and detected outliers for each plotId.

Usage

# S3 method for singleOut
plot(x, ..., plotIds = NULL, outOnly = TRUE, output = TRUE)

Value

A list of ggplot objects is invisibly returned.

Arguments

x

An object of class singleOut.

...

Ignored.

plotIds

A character vector of plotIds for which the outliers should be detected. If NULL, all plotIds in TP are used.

outOnly

Should only plots containing outliers be plotted?

output

Should the plot be output to the current device? If FALSE only a (list of) ggplot object(s) is invisibly returned. Ignored if outFile is specified.

See Also

Other functions for detecting outliers for single observations: detectSingleOut(), detectSingleOutMaize(), removeSingleOut()

Examples

## Create a TP object containing the data from the Phenovator.
PhenovatorDat1 <- PhenovatorDat1[!PhenovatorDat1$pos %in%
                                 c("c24r41", "c7r18", "c7r49"), ]
phenoTP <- createTimePoints(dat = PhenovatorDat1,
                            experimentName = "Phenovator",
                            genotype = "Genotype",
                            timePoint = "timepoints",
                            repId = "Replicate",
                            plotId = "pos",
                            rowNum = "y", colNum = "x",
                            addCheck = TRUE,
                            checkGenotypes = c("check1", "check2",
                                               "check3", "check4"))

## Select a subset of plants, for example here 9 plants.
plantSel <- phenoTP[[1]]$plotId[1:9]
# Then run on the subset.
resuVatorHTP <- detectSingleOut(TP = phenoTP,
                               trait = "EffpsII",
                               plotIds = plantSel,
                               confIntSize = 3,
                               nnLocfit = 0.1)

## Visualize the prediction by choosing a single plant...
plot(resuVatorHTP, plotIds = "c21r24", outOnly = FALSE)
## ...or a subset of plants.
plot(resuVatorHTP, plotIds = plantSel, outOnly = FALSE)