corplot2 {pcot2} | R Documentation

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

### Description

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

### Usage

    corplot2(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

### References

S.Song and M.Black (2006) PCOT2: an R package for assessing expression changes in groups of related genes. Submitted to Bioinformatics.

### See Also

`pcot2`,`corplot`,`aveProbe`

### Examples

    library(multtest)
    library(hu6800)
    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")
    pvalue <- c(0.001, 0.72)
    library(KEGG)
    pname <- unlist(mget(sel, env=KEGGPATHID2NAME))
    main <- paste("KEGG", sel, ": ", pname, ": ", "P=", pvalue, sep="")
    for(i in 1:length(sel)){
    fname <- paste("corplot2-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]
    corplot2(golub, selgene, golub.cl, main=main[i])
    dev.off()
    }

[Package pcot2 version 1.2.0 Index]