plotTraits {ctl}

plotTraits - Trait vs Trait scatterplot, colored by the selected genetic locus

Description

Trait vs Trait scatterplot, colored by the selected genetic locus

Usage

plotTraits(genotypes, phenotypes, phenocol = c(1, 2), marker = 1, doRank = FALSE)

Arguments

genotypes

Matrix of genotypes. (individuals x markers)

phenotypes

Matrix of phenotypes. (individuals x phenotypes)

phenocol

Which phenotype column(s) should be plotted against each other, Default: phenotype 1 versus 2

marker

Which marker (column in genotypes) should be used to add genotype as a color of the dots.

doRank

Transform quantitative data into ranked data before analyzing the slope.

Details

TODO

Value

TODO

Note

TODO

Author(s)

Danny Arends [e-mail]
Maintainer: Danny Arends [e-mail]

References

TODO

See Also

• CTLscan - Main function to scan for CTL

• CTLsignificant - Significant interactions from a CTLscan

• CTLnetwork - Create a CTL network from a CTLscan

• image.CTLobject - Heatmap overview of a CTLscan

• plot.CTLscan - Plot the CTL curve for a single trait

Examples

  library(ctl)
  data(ath.metabolites)                 # Arabidopsis Thaliana data set

  plotTraits(ath.metab$genotypes, ath.metab$phenotypes, marker=75, doRank = TRUE)