# plot.summaryAlphaPart: plot.summaryAlphaPart.R In AlphaPart: Partition/Decomposition of Breeding Values by Paths of Information

## Description

A function to plot summary of partitioned breeding values.

## Usage

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21``` ```## 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

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35``` ```## 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[]\$abs) print(p[]\$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) ```

AlphaPart documentation built on March 25, 2020, 5:13 p.m.