為什么heatmap.2添加不需要的復制列？

Question

鑒於此數據，（可以在此處找到完整的數據： http : //pastebin.com/raw.php?i=6NTcnLj7 ）：

Probes  Gene.symbol ImmGen  FOO_YJ_06.ip    FOO_MI_06.ip    FOO_NL_06.id    FOO_YJ_06.id    FOO_MI_06.id    BAR_NN_06.ip    BAR_PR_06.ip    BAR_YJ_06.ip    BAR_MI_06.ip    BAR_NL_06.id    BAR_YJ_06.id    BAR_MI_06.id    BAR_NN_24.ip    BAR_PR_24.ip    BAR_YJ_24.ip    BAR_MI_24.ip    BAR_NN_06.ip    BAR_NN_24.ip    BAR_PR_06.ip    BAR_PR_24.ip    BAR_YJ_06.ip    BAR_YJ_24.ip    BAR_MI_06.ip    BAR_MI_24.ip    BAR_NL_06.id    BAR_YJ_06.id    BAR_MI_06.id    TXT_NL_06.id    TXT_YJ_06.ip    TXT_MI_06.ip    TXT_YJ_06.id    TXT_MI_06.id    XXX_YJ_06.ip    XXX_MI_06.ip    XXX_NL_06.id    XXX_YJ_06.id    XXX_MI_06.id    KTH_NL_06.id    KTH_YJ_06.ip    KTH_MI_06.ip    K3_YJ_06.id K3_MI_06.id UUU_YJ_06.in    UUU_MI_06.in    DAR_NL_06.id    DAR_YJ_06.id    DAR_MI_06.id
1425352_at  Rcor3   StromalCells(12.99),DendriticCells(12.18),StemCells(11.43),NKCells(10.50),Macrophages(10.11),abTcells(9.11),Neutrophils(8.72),Monocytes(8.63),Bcells(8.61),gdTCells(7.71)   1.162   0.795   0.695   0.701   1.085   1.052   1.544   0.75    1.305   1.213   1.142   0.814   0.79    0.89    1.691   1.013   1.052   0.79    1.544   0.89    0.75    1.691   1.305   1.013   1.213   1.142   0.814   1.556   0.744   1.22    1.239   1.164   0.827   1.203   0.778   0.929   0.95    0   0.877   0.906   1.294   0.904   0   1.2 0.927   0.704   1.181
1417466_at  Rgs5    StromalCells(72.03),Neutrophils(3.39),DendriticCells(3.31),NKCells(3.28),Monocytes(3.25),Macrophages(3.15),gdTCells(3.01),abTcells(2.99),Bcells(2.80),StemCells(2.80)   1.149   0.904   1.225   0.821   1.075   0.947   0.969   1.262   0.868   1.013   0.984   0.938   0.925   1.11    1.36    1.014   0.947   0.925   0.969   1.11    1.262   1.36    0.868   1.014   1.013   0.984   0.938   0.877   0.887   1.035   1.226   0.979   1.142   1.126   0.933   0.854   1.033   0.911   1.255   1.038   1.125   1.086   1.18    0.958   1.115   1.017   1.061

我獲得此熱圖，僅以尾部顯示。 請注意，它添加了多余的多余復制列（標有紅色框）。

例如， BAR_YJ_06.ip在上面的數據中僅出現一次。 但是在情節中它出現了兩次BAR_YJ_06.ip和BAR_YJ_06.ip.1

這是為什么？ 我該如何去除它們？

這是我用來生成上圖的代碼：

#!/usr/bin/env Rscript

library(gplots);
library(RColorBrewer);


plot_hclust  <- function(inputfile,clust.height,type.order=c(),row.margins=30) {

    dat.bcd <- read.table(inputfile,na.strings=NA, sep="\t",header=TRUE);
    base <- substr(basename(inputfile), 1, nchar(basename(inputfile)) - 4 )
    rownames(dat.bcd) <- do.call(paste,c(dat.bcd[c("Probes","Gene.symbol","ImmGen")],sep=" "))
    dat.bcd <- dat.bcd[,!names(dat.bcd) %in% c("Probes","Gene.symbol","ImmGen")] 
    dat.bcd <- dat.bcd

    # Clustering and distance function
    hclustfunc <- function(x) hclust(x, method="complete")
    distfunc <- function(x) dist(x,method="maximum")


    # Select based on FC, as long as any of them >= anylim

    anylim <- 2.0
    dat.bcd <- dat.bcd[ apply(dat.bcd, 1,function(x) any (x >= anylim)), ]
    nrow(dat.bcd);

    #print(heatout):


    # Clustering functions
    height <- clust.height; 

    # Define output file name
    heatout <- paste("myheatmap.pdf",sep="");

print(heatout)

    # Compute distance and clusteirn function
    d.bcd <- distfunc(dat.bcd)
    fit.bcd <- hclustfunc(d.bcd)


    # Plot the hierarchical dendogram without heatmap
    # Cluster by height
    #cutree and rect.huclust has to be used in tandem
    clusters <- cutree(fit.bcd, h=height) 
    nofclust.height <-  length(unique(as.vector(clusters)));

    myorder <- colnames(dat.bcd); 
    if (length(type.order)>0) {
     myorder <- type.order
    }

    # Define colors
    #hmcols <- rev(brewer.pal(11,"Spectral"));
    hmcols <- rev(redgreen(2750));
    selcol <- colorRampPalette(brewer.pal(12,"Set3"))
    selcol2 <- colorRampPalette(brewer.pal(9,"Set1"))
    sdcol= selcol(5);
    clustcol.height = selcol2(nofclust.height);


    # Plot heatmap
  pdf(file=heatout,width=50,height=80); 


   par(xaxs="i");
   # We do bi-clustering 
   heatmap.2(as.matrix(dat.bcd), trace='none', dendrogram='both',Colv=T, scale='row', 
           hclust=hclustfunc, distfun=distfunc, col=hmcols,
           symbreak=T,
           margins=c(15,200), keysize=0.5,
           labRow=rownames(dat.bcd),
           lwid=c(2,0.1,4), lhei=c(0.05,3),
           lmat=rbind(c(5,0,4),c(3,1,2)),
           RowSideColors=clustcol.height[clusters])
    dev.off();

}

# Plotting 
plot_hclust("http://pastebin.com/raw.php?i=6NTcnLj7",clust.height=3);

Answer 1

這不是heatmap.2問題。 所有這些重復的樣本都顯示在您的源數據框中。 您應該檢查您的工作流程，並修復將重復項引入數據的步驟。

另一種臨時解決方案是在繪制熱圖之前從數據框中刪除所有重復的列：

data <- read.table(file='http://pastebin.com/raw.php?i=6NTcnLj7', header=T)

# obtain the logical vector (TRUE/FALSE), where TRUE == duplicated elements
ind <- duplicated(t(data))

# retain only the unique columns
# ! == inverts the logical vector, so TRUE == unique elements
subset <- data[,!ind]