情节中缺少的部分，然后重新出现并在保存时覆盖整个情节？ （R，热图.2）

Question

我正在使用 heatmap.2 创建绘图，但是，保存到我的源文件夹的初始绘图缺少键和标题。

然后当我运行dev.off() 命令时，然后使用 Key 和 Title 覆盖原始图形？

例如，我将制作这样的情节：

这远非完美。但是当我运行dev.off() 关闭设备时（否则会出现许多其他错误）：

您在上面看到的是一个非常扭曲的 Key 和我的“XYZ”标题。

到底为什么它要创建两个文件，首先是一个带有我的矩阵的文件，然后用包含我的翻转键和我的标题的第二个文件覆盖它？我无法遵循逻辑。

我已经更新了我的操作系统、我的 R 版本、RStudio、我的所有软件包和未安装的 RStudio。似乎没有任何帮助。

如果您想尝试复制我的错误，这里是示例矩阵：

structure(c(1, 4, 5, 3, 3, 4, 6, 1, 7, 5, 5, 4, 4, 8, 1, 3, 9, 
2, 2, 9, 3, 1, 3, 4, 4, 5, 5, 5, 1, 4, 4, 3, 3, 3, 9, 1), .Dim = c(6L, 
6L))

这是我用来绘制示例数据的脚本。您需要提供 SourceDir 并确保将矩阵分配给名称“Matrix”。

if (!require("gplots")) {
  install.packages("gplots", dependencies = TRUE)
  library(gplots)
}
if (!require("RColorBrewer")) {
  install.packages("RColorBrewer", dependencies = TRUE)
  library(RColorBrewer)
}

my_palette <- colorRampPalette(c("snow", "yellow", "darkorange", "red"))(n = 399)


transition
    col_breaks = c(seq(0,1,length=100),    #white 'snow'
                   seq(2,4,length=100), # for yellow
                   seq(5,7,length=100), # for orange 'darkorange'
                   seq(8,9,length=100))    # for red


png(paste(SourceDir, "Heatmap_Test.png"),      
    width = 5*1000,       
    height = 5*1000,
    res = 300,           
    pointsize =15)

heatmap.2(Matrix,
          main =  paste("XYZ"), 
          notecol="black",
          key = "true" ,
          colsep = c(3, 6, 9),
          rowsep = c(3, 6, 9),
          labCol = NULL,
          labRow = NULL,
          sepcolor="white",
          sepwidth=c(0.08,0.08),
          density.info="none",  
          trace="none",         
          margins=c(1,1),     
          col=my_palette,       
          breaks=col_breaks,    
          dendrogram="none",     
          RowSideColors = c(rep("blue", 3), rep("orange", 3)),
          ColSideColors = c(rep("blue", 3), rep("orange", 3)),
          srtCol = 0 ,        
          asp = 1 ,         
          adjCol = c(NA, 0) , 
          adjRow = c(0, NA) , 
          #keysize =  2 ,  
          Colv = FALSE ,      
          Rowv =  FALSE ,    
          key.xlab = paste("Correlation") , 
          cexRow = (1.8) , 
          cexCol = (1.8) , 
          notecex = (1.5) , 
          lmat = rbind(c(0,0,0,0), c(0,0,2,0),c(0,1,3,0),c(0,0,0,0)) , 
          #par(ColSideColors = c(2,2)),
          lhei = c(1, 1, 3, 1) , 
          lwid = c(1, 1, 3, 1)) 

dev.off()

我非常感谢您对此问题的任何见解。

Answer 1

我相信这是因为我有不止 1 到 4 个元素，因为我添加的彩色行算作必须在显示矩阵中排列的附加元素。

因此：

mat = rbind(c(0,0,0,0), c(0,0,2,0),c(0,1,3,0),c(0,0,0,0)) , 
lhei = c(1, 1, 3, 1) , 
lwid = c(1, 1, 3, 1))

不再切黄油。经过一番折腾，我终于设法使以下布局起作用（在我的实际数据上，而不是我的示例数据上）。

lmat = rbind(c(0,4,5,0), c(0,0,2,0),c(0,1,3,0),c(0,0,6,0)) , 
lhei = c(0.4, 0.16, 3, 0.4) , # Alter dimensions of display array cell heighs
lwid = c(0.4, 0.16, 3, 0.4),

注意包含元素 5 和 6。

所以我的最终命令看起来像这样（注意会有很多其他的变化，但真正的进展发生在我在 5 和 6 中添加之后）：

png(paste(SourceDir, "XYZ.png"),         
    width = 5*1500,        
    height = 5*1500,
    res = 300,            # 300 pixels per inch
    pointsize =30)        

heatmap.2(CombinedMtx,
          main =  paste("XYZ"), # heat map title
          notecol="black",
          key = "true" ,# change font color of cell labels to black
          colsep = c(6, 12, 18),
          labCol = c(" "," "," ", "XX"," "," "," "," "," ", "YY"," "," "," "," "," ", "ZZ"," "," "," "," "," ", "QQ"),
          rowsep = c(6, 12, 18),
          labRow = c(" "," "," ", "XX"," "," "," "," "," ", "YY"," "," "," "," "," ", "ZZ"," "," "," "," "," ", "QQ"),
          sepcolor="white",
          sepwidth=c(0.08,0.08),
          density.info="none",  
          trace="none",         
          margins=c(1,1),     
          col=my_palette,      
          breaks=col_breaks,   
          dendrogram="none",     
          RowSideColors = c(rep("#deebf7", 6), rep("#1c9099", 6), rep("#addd8e", 6), rep("#fee391", 6)),
          ColSideColors = c(rep("#deebf7", 6), rep("#1c9099", 6), rep("#addd8e", 6), rep("#fee391", 6)),
          srtCol = 0 ,        
          asp = 1 ,         
          adjCol = c(1.5, -61.5) , 
          adjRow = c(0, -1.38), 
          offsetRow = (-59.5),
          keysize =  2 ,  
          Colv = FALSE ,     
          Rowv =  FALSE ,    
          key.xlab = NA , 
          key.ylab = NULL ,
          key.title = NA ,
          cexRow = (1.6) , 
          cexCol = (1.6) , 
          notecex = (1.5) , 
          cex.main = (20),
          lmat = rbind(c(0,4,5,0), c(0,0,2,0),c(0,1,3,0),c(0,0,6,0)) , 
          #par(ColSideColors = c(2,2)),
          lhei = c(0.4, 0.16, 3, 0.4) , # Alter dimensions of display array cell heighs
          lwid = c(0.4, 0.16, 3, 0.4),
          symkey = any(0.5 < 0, na.rm=FALSE) || col_breaks,
          key.par=list(mar=c(3.5,0, 1.8,0) )  #tweak specific key paramters
)
dev.off() 

另外，如果您不是每次都使用dev.off() 创建PNG 和enf 来启动它，那么它不会起作用。我相信这也可能导致我的困惑，并且可能在绘制热图之后，一旦运行 dev.off() 命令，就会绘制一些元素，从而导致热图被覆盖。

这个（用我的矩阵）创建这个图像。

我所做的是一种非常有趣的方式来标记我的块，但在我弄清楚如何让 ComplexHeatmap 正常工作之前，我会被 Heatmap.2 这样的黑客卡住。