04-Image: Idiogram Graphs

Description Usage Arguments Value Author(s) References Examples

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

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## 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)
## 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 CytobandData-class, which combines numerical data at cytoband resolution with information on the chromosomal locations of the cytobands.

chr

The specific chromosome you want to view, typically in c(1:22, "X", "Y"). if you want to see all the chromosomes at once then you can set chr = "all".

what

A vector or list containing the names of the numerical column(s) that you want to display from the data frame. The barplot method only shows a single data column at a time. The plots resulting from the image method change depending on whether you supply a vector or a list, as well as on the length. For more details, see the vignettes, espefcialy the image gallery.

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 chr = "all" to determine the number of rows to use to display different chromosomes. Must be an integer between 1 and 4.

labels

Only use when what is a character vector (not a list) and chr is mot equal to "all". Used to label differnt columns of displayed data.

axes

Logical value; should axes be displayed?

legend

Logicla value; should a legend be added to the plot.

sigcolumn

The three parameters sigcolumn, sigcut, and alpha are used as a set. The first names a numerical column in the data set used to define "significance". The second is a vector of cutoffs that mark levels of significance. The latter is a number between 0 and 255 denoting the transparency level assigned to the color for each significance level.

sigcut

See sigcolumn.

alpha

See sigcolumn.

debug

Logical value; should the method print out debugging information. Probably best to ignore.

height

An object of the CytobandData-class, which combines numerical data at cytoband resolution with information on the chromosomal locations of the cytobands.

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

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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")

RCytoGPS documentation built on Feb. 11, 2021, 3:01 a.m.