mppR (version 1.5.0)

plot_QxEC: plot QTLxEC effect

Description

Plot allowing the visualization of the QTL parental allelic effect variation given an environmental covariate (EC). The function plot the sensitivity curve of the parent allelic effects.

Usage

plot_QxEC(
  Qeff,
  EC,
  env_id = NULL,
  QTL,
  sign_thre = 0.05,
  EC_id = "EC",
  trait_id = "trait",
  main = "QTLxEC",
  col_vec = NULL,
  text_size = 14
)

Value

QTLxEC sensitivity plot

Arguments

Qeff

output from the function QTL_effect_main_QxEC.

EC

Numeric matrix containing the EC values of a single covariate with environments as row and EC as column.

env_id

Character vector specifying the environment names. By default, E1, ... En

QTL

Numeric value indicating which QTL to plot

sign_thre

Numeric value indicating the significance threshold for a parent sensitivity slope to be ploted. Default = 0.05

EC_id

Character string indicating the name of the environmental covariate. Default = 'EC'.

trait_id

Character string indicating the name of the trait. Default = 'trait'.

main

Character string title of the plot. Default = 'QTLxEC'

col_vec

Character vector specifying colors for the parent sensitivity lines. Default = NULL

text_size

Numerical value specifying the size of the text in the plot. Default = 14.

Author

Vincent Garin

Examples

if (FALSE) {

data(mppData_GE)

Qpos <- c("PZE.105068880", "PZE.106098900")

EC <- matrix(c(180, 310, 240, 280), 4, 1)
rownames(EC) <- c('CIAM', 'TUM', 'INRA', 'KWS')
colnames(EC) <- 'cum_rain'

Qeff <- QTL_effect_main_QxEC(mppData = mppData_GE,
                         trait = c('DMY_CIAM', 'DMY_TUM', 'DMY_INRA_P', 'DMY_KWS'),
                         env_id = c('CIAM', 'TUM', 'INRA', 'KWS'),
                         QTL = Qpos, EC = EC)

pl <- plot_QxEC(Qeff, EC = EC, env_id = c('CIAM', 'TUM', 'INRA', 'KWS'), 
                QTL = 2, EC_id = 'cum rain', trait_id = 'DMY')

}