plot.summaryAlphaPart: plot.summaryAlphaPart.R

In janaobsteter/alphaPart: Partition/Decomposition of Breeding Values by Paths of Information

Description

A function to plot summary of partitioned breeding values.

Usage

## S3 method for class 'summaryAlphaPart'
plot(
  x,
  sortValue = TRUE,
  sortValueFUN = sum,
  sortValueDec = TRUE,
  addSum = TRUE,
  paths = NULL,
  xlab = NULL,
  ylab = NULL,
  xlim = NULL,
  ylim = NULL,
  color,
  lineSize = 1,
  lineType = 1,
  lineTypeList = NULL,
  useDirectLabels = TRUE,
  method = list(last.qp, hjust = 0),
  labelPath = NULL,
  ...
)

Arguments

x	summaryAlphaPart, object from the AlphaPart(...) or summary(AlphaPart(...), ...) call.
sortValue	Logical, affect legend attributes via sort of paths according to sortValueFUN function; if not logical, then ordered paths are given as a character vector.
sortValueFUN	Function, that produces single value for one vector, say mean or sum.
sortValueDec	Logical, sort decreasing.
addSum	Logical, plot the overall trend.
paths	Character or list or characters, name of paths to plot; if NULL plot all paths; see examples.
xlab	Character, x-axis label.
ylab	Character, y-axis label; can be a vector of several labels if there are more traits in x (recycled!).
xlim	Numeric, a vector of two values with x-axis limits; use a list of vectors for more traits.
ylim	Numeric, a vector of two values with y-axis limits; use a list of vectors for more traits.
color	Character, color names; by default a set of 54 colors is predefined from the RColorBrewer package; in addition a black colour is attached at the begining for the overall trend; if there are more paths than colors then recycling occours.
lineSize	Numeric, line width.
lineType	Numeric, line type (recycled); can be used only if lineTypeList=NULL.
lineTypeList	List, named list of numeric values that help to point out a set of paths (distinguished with line type) within upper level of paths (distinguished by, color), e.g., lineTypeList=list("-1"=1, "-2"=2, def=1) will lead to use of line type 1 for paths having "-1" at the end of path name and line type 2, for paths having "-2" at the end of path name, while line type 1 (default) will, be used for other paths; specification of this argument also causes recycling of colors for the upper level of paths; if NULL all lines have a standard line type, otherwise lineType does not have any effect.
useDirectLabels	Logical, use directlabels package for legend.
method	List, method for direct.label.
labelPath	Character, legend title; used only if useDirectLabels=FALSE.
...	Arguments passed to other functions (not used at the moment).

Details

Information in summaries of partitions of breeding values can be overhelming due to a large volume of numbers. Plot method can be used to visualise this data in eye pleasing way using ggplot2 graphics.

Value

A list of ggplot objects that can be further modified or displayed. For each trait in x there is one plot visualising summarized values.

Examples

## Partition additive genetic values by country
(res <- AlphaPart(x=AlphaPart.ped, colPath="country", colBV=c("bv1", "bv2")))

## Summarize population by generation (=trend)
(ret <- summary(res, by="gen"))

## Plot the partitions
p <- plot(ret, ylab=c("bv for trait 1", "bv for trait 2"), xlab="Generation")
print(p[[1]]$abs)
print(p[[2]]$abs)
print(p)

## Partition additive genetic values by country and sex
AlphaPart.ped$country.gender <- with(AlphaPart.ped, paste(country, gender, sep="-"))
(res <- AlphaPart(x=AlphaPart.ped, colPath="country.gender", colBV=c("bv1", "bv2")))

## Summarize population by generation (=trend)
(ret <- summary(res, by="gen"))

## Plot the partitions
p <- plot(ret, ylab=c("BV for trait 1", "BV for trait 2"), xlab="Generation")
print(p)
p <- plot(ret, ylab=c("BV for trait 1", "BV for trait 2"), xlab="Generation",
        lineTypeList=list("-1"=1, "-2"=2, def=3))
print(p)
p <- plot(ret, ylab=c("BV for trait 1", "BV for trait 2"), xlab="Generation",
        lineTypeList=list("-1"=1, "-2"=2, def=3), useGgplot2=FALSE, useDirectLabels = FALSE)
print(p)

## Plot control (color and type of lines + limits)
p <- plot(ret, ylab=c("BV for trait 1", "BV for trait 2"), xlab="Generation",
        useGgplot2=TRUE, color=c("green", "gray"), lineType=c(2, 3),
        sortValue=FALSE, lineSize=4,
        xlim=c(-1, 7))
print(p)

janaobsteter/alphaPart documentation built on March 25, 2020, 12:50 p.m.