fullfact (version 1.0)

barMANA: 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 bootstrap resampling results
data(chinook_bootS) #Chinook salmon offspring survival
#Extract un-corrected confidence interval
survival_ci<- ciMANA(comp=chinook_bootS,trait="survival")
survival_ci

#Default plot
barMANA(ci_dat=survival_ci)
#Add plot modifications
barMANA(ci_dat=survival_ci,bar_len=0.3,yunit=5,ymax=20,cex_ylab=1.3)

##Import jackknife resampling results
data(chinook_jackL)  #Chinook salmon offspring length
#Extract jackknife confidence interval
length_ci<- ciJack2(comp=chinook_jackL,full=c(0.0000000,0.7192253,0.2029684,1.0404425,
0.1077423),position="tray",trait="length")
length_ci

#Default plot
barMANA(ci_dat=length_ci)
#Add plot modifications
barMANA(ci_dat=length_ci,bar_len=0.3,yunit=20,ymax=100,cex_ylab=1.3)

##Group survival and length together in the same plot
data(chinook_bootL) #Chinook salmon offspring length
length_ci2<- ciMANA2(comp=chinook_bootL,position="tray",trait="length")
length_ci2
#
comb_r<- rbind(survival_ci$raw,length_ci2$raw)
comb_p<- rbind(survival_ci$percentage,length_ci2$percentage)
comb_ci<- list(raw=comb_r,percentage=comb_p)

#Default plot
barMANA(ci_dat=comb_ci)
#Add plot modifications
barMANA(ci_dat=comb_ci,bar_len=0.3,yunit=20,ymax=100,cex_ylab=1.3,leg="topleft")