ctl.lineplot {ctl}R Documentation

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 Danny.Arends@gmail.com
Maintainer: Danny Arends Danny.Arends@gmail.com

See Also

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)
  }

[Package ctl version 1.0.0-7 Index]