plotGenome {CNAnorm} | R Documentation |
plotGenome
plot normalized ratio and optionally segmented and/or smoothed
normalized ratio values in Package ‘CNAnorm’. It also shows annotation.
## S4 method for signature 'CNAnorm' plotGenome(object, maxRatio = 8, minRatio = -1, superimpose = character(0), gPar = NULL, numHorLables = 10, colorful = FALSE, show.centromeres = TRUE, idiogram = NULL, fixVAxes = FALSE, supLineColor = character(0), supLineCex = character(0), dot.cex = .2, ...)
object |
An object of Class |
maxRatio |
The maximum ratio to be shown on the plot. Values or ratio greater than maxRatio will be displayed as green triangulars |
minRatio |
The minimum ratio to be shown on the plot. Values or ratio smaller than minRatio will be displayed as green triangulars |
superimpose |
A character verctor with one or both of the following:
|
numHorLables |
. Number of maximum horizontal lables. The function will try to annotate numHorLables so that they are approximately equally spaced. |
colorful |
A switch to decide if the background dots representing the ratio of each window should be gray or colored according their value in relation to the peak closest to the median |
show.centromeres |
A switch to decide if location of centromere are displayed on the graph. The location of the centromere is stored in idiogram |
idiogram |
A data frame containing banding information. if NULL -default- human information will be loaded by data(hg19_hs_ideogr) |
fixVAxes |
A switch to decide if the vertical axes should be fixed to minRatio and maxRatio or fit the data within minRatio and maxRatio. |
gPar |
a S3 object with all graphical parameters. If NULL (default) data(gPar) is called |
supLineColor |
A three element character vector with colors to be used for
|
supLineCex |
A two element vector with |
dot.cex |
size of the dots in the plot |
... |
Further arguments to pass to the function |
An object of class "CNAnorm"
Stefano Berri s.berri@leeds.ac.uk and Arief Gusnanto a.gusnanto@leeds.ac.uk
plot
, par
, peakPloidy
,
gPar
, hg19_hs_ideogr
data(CN) # see peakPloidy documentation to know how object CN is created CN <- addDNACopy(CN) CN <- validation(CN) CN <- discreteNorm(CN) plotGenome(CN, superimpose = 'DNACopy')