corplot2                package:pcot2                R Documentation

_P_r_o_d_u_c_e _a _p_l_o_t _f_o_r _j_o_i_n_t_l_y _v_i_s_u_a_l_i_z_i_n_g _u_n_p_o_o_l_e_d _c_o_r_r_e_l_a_t_i_o_n
_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

_R_e_f_e_r_e_n_c_e_s:

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

_S_e_e _A_l_s_o:

     'pcot2','corplot','aveProbe'

_E_x_a_m_p_l_e_s:

     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()
     }

