plot_QxEC: plot QTLxEC effect

In vincentgarin/mppR: Multi-Parent Population QTL Analysis

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
)

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.

Value

QTLxEC sensitivity plot

Author(s)

Vincent Garin

Examples

## Not run: 

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')


## End(Not run)

vincentgarin/mppR documentation built on March 13, 2024, 7:30 p.m.