ctl.lineplot: Lineplot CTL on multiple traits

In ctl: Correlated Trait Locus Mapping

Lineplot CTL on multiple traits

Description

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

Usage

ctl.lineplot(CTLobject, mapinfo, phenocol, significance = 0.05, gap = 50, 
col = "orange", bg.col = "lightgray", cex = 1, verbose = FALSE)

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 (only significant markers will be annotated).
phenocol	Which phenotype results to plot. Defaults to plot all phenotypes.
significance	Significance threshold to set a genome wide False Discovery Rate (FDR).
gap	The gap between chromosomes in cM.
col	Line color used.
bg.col	Node background color.
cex	Global magnificantion factor for the image elements.
verbose	Be verbose.

Details

None.

Value

None.

Author(s)

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

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

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

  todo <- c(1,3,4,5,6,8,9,10,11,12,14,17,18,19,22,23)
  op   <- par(mfrow = c(4,4))
  op   <- par(oma = c(0.1,0.1,0.1,0.1))
  op   <- par(mai = c(0.1,0.1,0.1,0.1))
  for(x in todo){ # Overview of the 16 traits with CTLs
    ctl.lineplot(ath.result, ath.metab$map, phenocol = x, sign=0.1)
  }

ctl documentation built on Nov. 27, 2023, 5:09 p.m.