qq.evaluate.core {EvaluateCore}R Documentation

Quantile-Quantile Plots

Description

Plot Quantile-Quantile (QQ) plots (Wilk and Gnanadesikan 1968) to graphically compare the probability distributions of quantitative traits between entire collection (EC) and core set (CS).

Usage

qq.evaluate.core(data, names, quantitative, selected)

Arguments

data

The data as a data frame object. The data frame should possess one row per individual and columns with the individual names and multiple trait/character data.

names

Name of column with the individual names as a character string

quantitative

Name of columns with the quantitative traits as a character vector.

selected

Character vector with the names of individuals selected in core collection and present in the names column.

Value

A list with the ggplot objects of QQ plots of CS vs EC for each trait specified as quantitative.

References

Wilk MB, Gnanadesikan R (1968). “Probability plotting methods for the analysis for the analysis of data.” Biometrika, 55(1), 1–17.

See Also

qqplot

Examples


####################################
# Use data from R package ccChooser
####################################

library(ccChooser)
data("dactylis_CC")
data("dactylis_EC")

ec <- cbind(genotypes = rownames(dactylis_EC), dactylis_EC[, -1])
ec$genotypes <- as.character(ec$genotypes)
rownames(ec) <- NULL
ec[, c("X1", "X6", "X7")] <- lapply(ec[, c("X1", "X6", "X7")],
                                    function(x) cut(x, breaks = 4))
ec[, c("X1", "X6", "X7")] <- lapply(ec[, c("X1", "X6", "X7")],
                                    function(x) factor(as.numeric(x)))
head(ec)

core <- rownames(dactylis_CC)

quant <- c("X2", "X3", "X4", "X5", "X8")
qual <- c("X1", "X6", "X7")

####################################
# EvaluateCore
####################################

qq.evaluate.core(data = ec, names = "genotypes",
                 quantitative = quant, selected = core)



[Package EvaluateCore version 0.1.2 Index]