CytobandData-methods {RCytoGPS} | R Documentation |
Idiogram Graphs
Description
The image
and barplot
methods of the
CytobandData-class
provide flexible displays of genome
wide data that has been summarized at cytoband resolution.
Usage
## S4 method for signature 'CytobandData'
image(x, chr, what,
pal = palette(), nrows = 2, labels = NULL,
horiz = FALSE, axes = chr != "all", debug = FALSE, legend = FALSE,
sigcolumn = NA, sigcut = 0.01, alpha = 63, clip = FALSE)
## S4 method for signature 'CytobandData'
barplot(height, what, col = "blue", altcol = "#FED4C4",
ylab = "Percent", hline = NULL,
xform = function(x) x, ...)
Arguments
x |
An object of the |
chr |
The specific chromosome you want to view, typically in
|
what |
A vector or list containing the names of the numerical
column(s) that you want to display from the data frame. The
|
pal |
a charcter vector containing the colors you want to use for different data shown in the plot. |
horiz |
A logical value determining whether images present the chromosome idiograms horizontally or vertically. |
nrows |
Only used when |
labels |
Only use when |
axes |
Logical value; should axes be displayed? |
legend |
Logicla value; should a legend be added to the plot. |
sigcolumn |
The three parameters |
sigcut |
See |
alpha |
See |
clip |
A logical value; should te length of the chromosome fill the device (if TRUE) or be plotted relative to the length of Chromosome 1 (if FALSE). Currently only used when plotting two values, one on either side of a single chromosome. |
debug |
Logical value; should the method print out debugging information. Probably best to ignore. |
height |
An object of the |
col |
a character vector containing the colors you want to use for different data shown in the plot. |
altcol |
Determines the color used, lternating with white, in the x-axis plot of all chromosomes. |
ylab |
Label for the y-axis in a barplot. |
hline |
Numeric vector of heights at which toadd a horizontal line. |
xform |
Function to transform the data before plotting. Defauly is the identity map, which does nothing. |
... |
Ignored. |
Value
Both the image
and barplot
methods invisibly return
their first argument, and object fo the CytobandData
class.
Author(s)
Kevin R. Coombes krc@silicovore.com, Dwayne G. Tally dtally110@hotmail.com
References
Abrams ZB, Tally DG, Coombes KR. RCytoGPS: An R Package for Analyzing and Visualizing Cytogenetic Data. In preparation.
Abrams ZB, Tally DG, Zhang L, Coombes CE, Payne PRO, Abruzzo LV, Coombes KR. Pattern recognition in lymphoid malignancies using CytoGPS and Mercator. Under review.
Examples
jsonDir <- system.file("Examples/JSONfiles", package = "RCytoGPS")
x <- readLGF(folder = jsonDir)
cytoData <- data.frame(x[["CL"]], x[["frequency"]])
bandData <- CytobandData(cytoData)
datacolumns <- names(x[["frequency"]])
barplot(bandData, what = datacolumns[1], col="forestgreen")
image(bandData, what = datacolumns[1:3], chr = 2)
image(bandData, what = datacolumns[1:3], chr = "all")
image(bandData, what = as.list(datacolumns[1:2]), chr = 2)
image(bandData, what = as.list(datacolumns[1:2]), chr = "all")