plotNormalizedData: plot estimated absolute levels of two conditions

In CALIB: Calibration model for estimating absolute expression levels from microarray data

Description

plot estimated absolute levels of any two user-specified conditions. The values in the plot are in log scale.

Usage

plotNormalizedData(data, condition = c(1, 2), xlab = NULL, ylab = NULL,
                   main = NULL,xlim = NULL, ylim = NULL, pch = 19,
                   cex = 0.2,col = "black", diag=TRUE, diagcol="blue",
                   diaglwd=1.5, ...)

Arguments

data	matrix containing estimated absolute levels. columns are conditons and rows are genes.
condition	integer vector giving the two conditions to be plotted.
xlab	a title for the x axis.
ylab	a title for the y axis.
main	an overall title for the plot.
xlim	the x limits (min,max) of the plot.
ylim	the y limits of the plot.
pch	an integer code for one of a set of plotting characters or symbols for the spike data set. Default is 19.
cex	a numerical value giving the amount by which points should be scaled relative to the default. Default is 0.2.
col	the color of the points. Default is black.
diag	a logical value. Add diagonal on the plot if it is TRUE. Default is TRUE.
diagcol	the color of the diagonal. Default is blue.
diaglwd	the width of the diagonal. Default is 1.5.
...	other graphical parameters can be used in function plot.

Details

The function polts estimated absolute expression levels of two conditions. It accepts expression levels from the argument 'data', which should have the same data format as the output value of the function normalizeData.

The two conditions to be plotted should be specified by the argument condition. The condition should be a numeric vector with length two and it should be subset of condition vector of the design matrix. see function NormalizeData.

see other graphic functions for the other arguments.

Value

A plot is created on the current graphics device.

Author(s)

Hui Zhao

Examples

# load data: normalized data
data(normdata)
	
# specify the two conditions to be plotted.
cond <- c(1,2)
	
# use the default values for other parameters.
plotNormalizedData(normdata,condition = cond)

CALIB documentation built on Oct. 31, 2019, 3:45 a.m.