barMANA: Bargraph of confidence intervals

In fullfact: Full Factorial Breeding Analysis

Bargraph of confidence intervals

Description

A simple bargraph function for confidence intervals of additive genetic, non-additive genetic, and maternal variance components. Also, plots the median for the bootstrap resampling method or mean of the pseudo-values for the jackknife resampling method.

Usage

barMANA(ci_dat, type = "perc", bar_len = 0.1, ymax = NULL, ymin = NULL, yunit = NULL,
leg = "topright", cex_ylab = 1, cex_yaxis = 1, cex_names = 1)

Arguments

ci_dat	Data frame of a confidence interval function.
type	Default is "perc" for percentage values of variance components. Other option is "raw" for raw values of variance components.
bar_len	Length of error bar in inches.
ymax	Maximum value of the y-axis.
ymin	Minimum value of the y-axis.
yunit	Unit increment of the y-axis.
leg	Position of the simple legend.
cex_ylab	Magnification of the y-axis label.
cex_yaxis	Magnification of the y-axis units.
cex_names	Optional magnification of trait labels.

Details

Plots a bargraph with the median or mean as the top of the shaded bar and error bars covering the range of the confidence interval. Uses an object produced by any of the bootstrap resampling CI functions, i.e. ciMANA, ciMANA2, and ciMANA3 or jackknife resampling functions, i.e. ciJack, ciJack2, and ciJack3. The median is plotted for bootstrap resampling and the mean of pseudo-value for jackknife resampling. Produces a simple legend. The function can plot several bar graphs grouped by label to visualize several phenotypic traits.

Examples

##Import jackknife resampling results
data(chinook_jackL) #Chinook salmon length
length_ci<- ciJack(comp=chinook_jackL,full=c(0,0.7192,0.2030,1.0404))
barMANA(ci_dat=length_ci)  #default plot
barMANA(ci_dat=length_ci,bar_len=0.3,yunit=20,ymax=100,cex_ylab=1.3) 

##Group length and survival together in the same plot
data(chinook_bootS) #Chinook salmon survival (bootstrap resampling)
length_ci<- ciJack(comp=chinook_jackL,full=c(0,0.7192,0.2030,1.0404),trait="length")
survival_ci<- ciMANA(comp=chinook_bootS,trait="survival")
colnames(length_ci$raw)[3]<- "median"; colnames(length_ci$percentage)[3]<- "median"
comb_bar<- list(raw=rbind(length_ci$raw,survival_ci$raw),
percentage=rbind(length_ci$percentage,survival_ci$percentage))
#
barMANA(ci_dat=comb_bar) #default plot
barMANA(ci_dat=comb_bar,bar_len=0.3,yunit=20,ymax=100,cex_ylab=1.3)

fullfact documentation built on May 29, 2024, 1:21 a.m.