ctl (version 1.0.0-10)

ctl.circle: Circleplot CTL on multiple traits

Description

Plot the CTL for genome-wide CTL on multiple traits (the output of CTLscan).

Usage

ctl.circle(CTLobject, mapinfo, phenocol, significance = 0.05, gap = 50, cex = 1,
verbose = FALSE)

Value

None.

Arguments

CTLobject

An object of class "CTLobject", as output by CTLscan.

mapinfo

The mapinfo matrix with 3 columns: "Chr" - the chromosome number, "cM" - the location of the marker in centiMorgans and the 3rd column "Mbp" - The location of the marker in Mega basepairs. If supplied the marker names (rownames) should match those in the CTLobject.

phenocol

Which phenotype results to plot. Defaults to plot all phenotypes.

significance

Significance threshold to set a genome wide False Discovery Rate (FDR).

gap

Gap between chromosomes in cM.

cex

Global magnificantion factor for the image elements.

verbose

Be verbose.

Author

Danny Arends
Maintainer: Danny Arends

Details

None.

See Also

• CTLscan - Scan for CTL

• CTLprofiles - Extract CTL interaction profiles

• print.CTLscan - Print a summary of a CTLscan

• par - Plot parameters

• colors - Colors used in plotting

Examples

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

  ctl.circle(ath.result, ath.metab$map, sign=0.001)
  ctl.circle(ath.result, ath.metab$map, phenocol = 1:6, sign = 0.01)