为什么heatmap.2添加不需要的复制列？

Question

鉴于此数据，（可以在此处找到完整的数据： 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

我获得此热图，仅以尾部显示。 请注意，它添加了多余的多余复制列（标有红色框）。

例如， BAR_YJ_06.ip在上面的数据中仅出现一次。 但是在情节中它出现了两次BAR_YJ_06.ip和BAR_YJ_06.ip.1

这是为什么？ 我该如何去除它们？

这是我用来生成上图的代码：

#!/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

这不是heatmap.2问题。 所有这些重复的样本都显示在您的源数据框中。 您应该检查您的工作流程，并修复将重复项引入数据的步骤。

另一种临时解决方案是在绘制热图之前从数据框中删除所有重复的列：

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]