plotGW: Plot genome-wide data along the genome

In lol: Lots Of Lasso

Description

Plot different measurements across the genome such as copy number amplifications and deletions.

Usage

plotGW(data, pos, marks=NULL, fileType='png', file='plotGW', width=1000, height=500,  autoscale=FALSE, col=c('lightblue', 'lightgreen', 'darkblue', 'darkgreen'), legend=1:10, ylab='', pch=19, cex.axis=1.2 ,cex.lab=1.2, cex=.5, legend.pos='bottomright', mtext=NULL, mtext.side=2, mtext.at=NULL, mtext.line=3, ...)

Arguments

data	data matrix to plot, each column is plotted individually across the genome
pos	the chromosome locations for the data, can be a matrix or data frame with a column named chromosome_name, or a numeric vector
marks	if there is specific marks to plot on the baselne, eg. to indicate where are the SNPs, should be a vector of numbers indicating where the marks is relative to the input data matrix
fileType	either png or pdf file type
file	file name
width	width of the plot
height	height of the plot
autoscale	should the columns of data be scaled?
col	colors for each of the data columns to be plotted, should be no shorter than the number of columns in 'data'
legend	legend text in the legend box
ylab	parameter for par, default to ”
pch	parameter for par, default to 19
cex.axis	parameter for par, default to 1.2
cex.lab	parameter for par, default to 1.2
cex	parameter for par, default to 0.5
legend.pos	parameter for legend, default to 'bottomright'
mtext	parameter for mtext, default to NULL
mtext.side	parameter for mtext, default to 2
mtext.at	parameter for mtext, default to 2
mtext.line	parameter for mtext, default to 3
...	Other parameters to pass to plot() or legend()

Details

This function requires as input data a vector or a matrix with different variables in columns, and a position matrix of chromosome name and start position. The number of rows in the position matrix should be the same as the length of the data vector or the number of rows of the data matrix. The function plots the data according to the position across the genome, providing a genome-wide description.

Value

Write an image file to disk, either in png or pdf format.

Author(s)

Yinyin Yuan

See Also

lasso.cv

Examples

data(chin07)
gain <- rowSums(chin07$cn >= .2)
loss <- -rowSums(chin07$cn <= -.2)
plotGW(data=cbind(gain, loss), pos=attr(chin07$cn, 'chrome'), legend=c('gain', 'loss'))

lol documentation built on Oct. 31, 2019, 2:21 a.m.