data_effects: Get effects information

In viewpoly: A Shiny App to Visualize Genetic Maps and QTL Analysis in Polyploid Species

Get effects information

Description

Get effects information

Usage

data_effects(
  qtl_info,
  effects,
  pheno.col = NULL,
  parents = NULL,
  lgs = NULL,
  groups = NULL,
  position = NULL,
  software,
  design = c("bar", "circle", "digenic")
)

Arguments

qtl_info	data.frame with: LG - linkage group ID; Pos - position in linkage map (cM); Pheno - phenotype ID; Pos_lower - lower position of confidence interval; Pos_upper - upper position of the confidence interval; Pval - QTL p-value; h2 - herdability
effects	data.frame with: pheno - phenotype ID; qtl.id - QTL ID; haplo - haplotype ID; effect - haplotype effect value
pheno.col	integer identifying phenotype
parents	vector with parents ID
lgs	vector of integers with linkage group ID of selected QTL/s
groups	vector of integers with selected linkage group ID
position	vector of centimorgan positions of selected QTL/s
software	character defining which software was used for QTL analysis. Currently support for: QTLpoly, diaQTL and polyqtlR.
design	character defining the graphic design. Options: 'bar' - barplot of the effects; 'circle' - circular plot of the effects (useful to compare effects of different traits); 'digenic' - heatmap plotting sum of additive effects (bottom diagonal) and digenic effects (top diagonal) when present

Value

ggplot graphic

viewpoly documentation built on Nov. 2, 2022, 1:05 a.m.