ctl.circle | R Documentation |
Plot the CTL for genome-wide CTL on multiple traits (the output of CTLscan
).
ctl.circle(CTLobject, mapinfo, phenocol, significance = 0.05, gap = 50, cex = 1,
verbose = FALSE)
CTLobject |
An object of class |
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. |
None.
None.
Danny Arends Danny.Arends@gmail.com
Maintainer: Danny Arends Danny.Arends@gmail.com
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
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)
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