corplot2                package:pcot2                R Documentation

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_i_n_f_o_r_m_a_t_i_o_n _a_n_d _e_x_p_r_e_s_s_i_o_n _d_a_t_a _f_o_r _s_e_l_e_c_t_e_d _g_e_n_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     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.

_U_s_a_g_e:

     corplot2(x, sel, cla = NULL, inputP = NULL, main, gene.locator = FALSE, add.name = TRUE, font.size = 1, dist.method = "euclidean")

_A_r_g_u_m_e_n_t_s:

       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.

_A_u_t_h_o_r(_s):

     Sarah Song and Mik Black

_S_e_e _A_l_s_o:

     'pcot2','corplot','aveProbe'

_E_x_a_m_p_l_e_s:

     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")
     pvalue <- c(0.001, 0.72)
     library(KEGG.db)
     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()
     }

