draw.crossplots {CIS.DGLM}

Draw Crossplots

Description

This function draws crossplots for As and Bs in each variable in the mean and variance models with the Mean Estimate vs Standard Deviation Estimate.

Usage

draw.crossplots(
  fn.mean.A,
  fn.mean.B,
  fn.sd.A,
  fn.sd.B,
  fn.pe.mean,
  fn.pe.sd,
  variables,
  ishybrid,
  num.vars
)

Arguments

fn.mean.A

Enter file name of file with confidence intervals of mean stress, environment level A data. Can be hybrid, inbred, or full data set. This file needs to be obtained from the bootstrap function, run with the desired data set.

fn.mean.B

Enter file name of file with confidence intervals of mean stress, environment level B data. Can be hybrid, inbred, or full data set. This file needs to be obtained from the bootstrap function, run with the desired data set.

fn.sd.A

Enter file name of file with confidence intervals of SD stress, environment level A data. Can be hybrid, inbred, or full data set. This file needs to be obtained from the bootstrap function, run with the desired data set.

fn.sd.B

Enter file name of file with confidence intervals of SD stress, environment level B data. Can be hybrid, inbred, or full data set. This file needs to be obtained from the bootstrap function, run with the desired data set.

fn.pe.mean

Enter file name of file with point estimates of mean for each gene (both A and B environment levels present). Can be hybrid, inbred, or full data set. This file needs to be obtained from the mean_stress function, run with the desired data set.

fn.pe.sd

Enter file name of file with point estimates of SD for each gene (both A and B environment levels present). Can be hybrid, inbred, or full data set. This file needs to be obtained from the sd.stress function, run with the desired data set.

variables

List of variables from mean and variance models. Mean variables need to be listed first, then variance variables.

ishybrid

Indicates the type of the data set being examined. You can use 'Hybrid', 'Inbred', "All", etc.

num.vars

Number of variables per model. Used to ascertain if a variable falls in the mean or the variance model.

Value

There is no return for this function; it prints crossplots for each of the variables listed in the parameter 'variables.'

Examples

test.data <- simu.inter.dat.interboth(n.rep = 3, n.obs.per.rep = 15, ran.seed = 1)
variables <- colnames(test.data[-1])
mean_stress(test.data, variables, 'stress')
sink();
sd.stress(test.data, variables, 'stress')
sink();
plot_vars <- c("loci_var.4","loci_var.7.env_var.2","loci_var.3",
"loci_var.5","loci_var.8.env_var.2","loci_var.4")
bootstrap(test.data, n.boot=100,variables, 'stress')
draw.crossplots('bootstrap mean A stress.txt','bootstrap mean B stress.txt',
'bootstrap sd A stress.txt', 'bootstrap sd B stress.txt', 'mean_stress.txt',
'sd_stress.txt', plot_vars, 'All',3)
unlink(c('bootstrap mean A stress.txt','bootstrap mean B stress.txt',
'bootstrap sd A stress.txt', 'bootstrap sd B stress.txt',
'mean_stress.txt', 'sd_stress.txt'))