image.CTLobject {ctl}

Plot genome-wide CTL on multiple traits

Description

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

Usage

## S3 method for class 'CTLobject'
image(x, marker_info, against = c("markers","phenotypes"), significance = 0.05,
col=whiteblack, do.grid=TRUE, grid.col = "white", verbose = FALSE, add=FALSE, 
breaks = c(0, 1, 2, 3, 10, 10000), ...)

Arguments

x

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

marker_info

Information used to plot chromosome lines.

against

Plot which interaction matrice, options are: markers: the phenotype*marker or phenotypes: the phenotype*phenotypes matrix.

significance

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

col

Color-range used in plotting.

do.grid

When TRUE, grid lines are added to the plot.

grid.col

Color used for the grid lines, only used when do.grid = TRUE.

verbose

Be verbose.

add

Add this plot to a previously opened plot window.

breaks

See par.

...

Passed to the function image when it is called.

Details

None.

Value

For a detailed description, see CTLprofiles

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

  library(ctl)
  data(ath.result)       # Arabidopsis Thaliana results
  #Phenotype to phenotype matrix
  p2p_matrix <- image(ath.result, against="phenotypes")
  #Phenotype to marker matrix
  p2m_matrix <- image(ath.result, against="markers")