dotplot-methods: dotplots on ExpressionSet objects

In drmjc/microarrays: A collection of microarray and genomic helper code.

Description

Plot either a single feature from an ExpressionSet as a dotplot (default is sorted low to high), or generate a 2D dotplot from combinations of 2 ExpressionSet's, or ExpressionSet and a named numeric, where those names overlap with the featureNames from the ExpressionSet. As always, the 2D objects need to have some overlap in their names, but otherwise, data unique to each set will be silently ignored.

Arguments

x	an ExpressionSet
y	an ExpressionSet, or missing.
sort	logical: if TRUE, then sort from low to high (default=TRUE). only applies if y is missing.
feature	the index or name of the feature to plot. default=1. In the 2D case, if the feature exists in both ExpressionSet's then that will be seleected. If plotting different features from x and y, then leave feature=1, and select the feature of interest from each expression set using '['. see examples.
xlab	see par
ylab	see par
main	see par
add.mean	logical: add a horizontal line about the mean of that feature
samples	an optional character vector of sample names to highlight and label in red.
lowess.col	the colour of the 2D loess line. NA to not show one, otherwise choose a named colour.

Value

nothing

2D dotplots

these are just xy plots; if x and or y is an ExpressionSet, then the first feature will be extracted from each; use the '[' operator to subset either x or y if necessary.

Author(s)

Mark Cowley, 2012-10-16

Examples

## Not run: 
	hent3 <- x["SLC29A3", ]
	dotplot(hent3, sort=T, samples="APGI_1966")

	dotplot(x, feature="SLC29A3", sort=T, samples="APGI_1966")

 num <- rnorm(80); names(num) <- sampleNames(x)[1:80]
 dotplot(hent3, num)
 dotplot(num, hent3)

 dotplot(x["BRCA2",], x["BRCA1", ])
 dotplot(x, x, feature="BRCA1")

## End(Not run)

drmjc/microarrays documentation built on May 15, 2019, 2:26 p.m.