image.CTLobject | R Documentation |
Plot the CTL for genome-wide CTL on multiple traits (the output of CTLscan
).
## 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), ...)
x |
An object of class |
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 |
None.
For a detailed description, see CTLprofiles
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
#Phenotype to phenotype matrix
p2p_matrix <- image(ath.result, against="phenotypes")
#Phenotype to marker matrix
p2m_matrix <- image(ath.result, against="markers")
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