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WGCNA-errorLength of 'xLabels' m

WGCNA-errorLength of 'xLabels' m

作者: 天涯清水 | 来源:发表于2020-02-12 22:50 被阅读0次

    Error in labeledHeatmap(Matrix = moduleTraitCor, xLabels = colnames(design), : Length of 'xLabels' must equal the number of columns in 'Matrix.'

    用以前的代码,跑其他的样本第5步的时候出现了

    STEP5:模块和性状的关系
    MEs是一个关于modules的特征量矩阵,行数等于筛选的modules数,列数等于样本数;

    if(T){
      nGenes = ncol(datExpr)
      nSamples = nrow(datExpr)
      design=model.matrix(~0+ datTraits$ClinicalTraits)
      colnames(design)=levels(datTraits$ClinicalTraits)
      moduleColors <- labels2colors(net$colors)
      # Recalculate MEs with color labels
      MEs0 = moduleEigengenes(datExpr, moduleColors)$eigengenes
      MEs = orderMEs(MEs0); ##不同颜色的模块的ME值矩 (样本vs模块)
      moduleTraitCor = cor(MEs, design , use = "p");
      moduleTraitPvalue = corPvalueStudent(moduleTraitCor, nSamples)
      
      sizeGrWindow(10,6)
      # Will display correlations and their p-values
      textMatrix = paste(signif(moduleTraitCor, 2), "\n(",
                         signif(moduleTraitPvalue, 1), ")", sep = "");
      dim(textMatrix) = dim(moduleTraitCor)
      png("step5-Module-trait-relationships.png",width = 800,height = 1200,res = 120)
      #pdf("step5-Module-trait-relationships.pdf",width = 36, height = 36)
      par(mar = c(6, 8.5, 3, 3));
      
      # Display the correlation values within a heatmap plot
      
      labeledHeatmap(Matrix = moduleTraitCor,
                     xLabels = colnames(design),
                     yLabels = names(MEs),
                     ySymbols = names(MEs),
                     colorLabels = FALSE,
                     colors = greenWhiteRed(50),
                     textMatrix = textMatrix,
                     setStdMargins = FALSE,
                     cex.text = 0.5,
                     zlim = c(-1,1),
                     main = paste("Module-trait relationships"))
      dev.off()
    }
    

    报错信息:

    Error in labeledHeatmap(Matrix = moduleTraitCor, 
    xLabels = colnames(design),  :    
    Length of 'xLabels' must equal the number of columns in 'Matrix.'
    

    出图的时候错了。搜索也找不到答案,不知道如何解决。

    colnames(design)的结果为null,把colnames(design)转化为因子也不能解决。

    今天(2020.02.13)把上面的问题解决了,的确是把colnames(design)转化为因子。准确的说应该是吧。design转化为因子。

    colnames(design)=levels(as.factor(datTraits$ClinicalTraits))

    但是会有警告信息,不过不影响结果:

    Warning message:
    In greenWhiteRed(50) :
      WGCNA::greenWhiteRed: this palette is not suitable for people
    with green-red color blindness (the most common kind of color blindness).
    Consider using the function blueWhiteRed instead.
    

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