plot_QTLxEC: plot QTLxEC effect

In mppR: Multi-Parent Population QTL Analysis

plot QTLxEC effect

Description

Plot allowing the visualisation of the QTL allelic effect given an environmental covariate (EC). It represents parental QTL effects that significantly interact with the EC. Those values are added to the (central) reference parent effect (intercept) which allow a comparison of the parental allele contribution with respect to the reference and in the scale of the trait.

Usage

plot_QTLxEC(
  Qeff,
  Q_id,
  RP = "RP",
  EC_id = "EC",
  trait_id = "trait",
  main = "QTLxEC",
  keep_par = NULL,
  rem_par = NULL,
  text_size = 14
)

Arguments

Qeff	output from the function QTL_effect_QxEC obtained with option QTLxEC_plot = TRUE.
Q_id	Numeric value indicating which QTL to plot
RP	Character string indicating the name of the reference (central) parent. Default = 'RP'.
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'
keep_par	Character vector or string specifying the only parents that should be ploted. Default = NULL.
rem_par	Character vector or string specifying the parents that should not be ploted. 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_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_QTLxEC(Qeff, Q_id = 2, RP = "UH007", EC_id = 'cum rain',
trait_id = 'DMY')


## End(Not run)

mppR documentation built on Jan. 6, 2023, 1:23 a.m.