Produce a plot for jointly visualizing pooled correlation information and expression data for selected genes

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Description

This plot is used for looking at pooled inter-gene correlation within a pre-defined group of genes, in conjunction with information about differences in expression activity between classes.

Usage

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corplot(x, sel, cla = NULL, inputP = NULL, main, gene.locator = FALSE, add.name = TRUE, font.size = 1, dist.method = "euclidean")

Arguments

x

A matrix with no missing values; Each row represents a gene and each column represents a sample.

sel

A vector of selected gene identifiers.

cla

Class labels representing two distinct experimental conditions (e.g., normal and disease).

inputP

This option allows users to input p-values for each gene (e.g., if produced by another software package).

main

A title for the plot.

gene.locator

This option allows users to click of the plot to identify groups of genes. Clicking twice on the diagonal of the plot returns the identifiers of genes between the points clicked.

add.name

Specifies whether gene identifiers should be printed on the plot.

font.size

Adjusts the size of gene names printed on the plot.

dist.method

Specifies the method for calculating inter-gene distance (used when ordering the rows and columns of the correlation plot). The available distance methods are "euclidean", "maximum", "manhattan", "canberra", "binary", "pearson","correlation" or "spearman". For additional details see the amap package and the help documentation for the Dist function.

Author(s)

Sarah Song and Mik Black

See Also

pcot2,corplot2,aveProbe

Examples

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library(multtest)
library(hu6800.db)  
data(golub)
rownames(golub) <- golub.gnames[,3]
colnames(golub) <- golub.cl
KEGG.list <- as.list(hu6800PATH)
imat <- getImat(golub, KEGG.list, ms=10) 
colnames(imat) <- paste("KEGG", colnames(imat), sep="")
sel <- c("04620","04120")
main <- paste("KEGG", sel, sep="")
for(i in 1:length(sel)){
fname <- paste("corplot-KEGG",sel[i] , ".jpg", sep="")
jpeg(fname, width=1600, height=1200, quality=100)
selgene <- rownames(imat)[imat[,match(paste("KEGG",sel,sep="")[i],colnames(imat))]==1]
corplot(golub, selgene, golub.cl, main=main[i])
dev.off()
}