零件从绘图中丢失，然后在保存时重新出现并覆盖整个绘图？ （R，Heatmap.2）

Question

我正在使用heatmap.2创建图，但是，保存到源文件夹的初始图缺少键和标题。

然后我运行dev.off()命令时，然后使用键和标题覆盖原始图形吗？

例如，我将生成如下图：

这还远非完美。但是然后当我运行dev.off()关闭设备时（否则会发生其他错误）：

您在上面看到的是一个非常变形的键和我的“ XYZ”标题。

为什么要创建两个文件，首先使用我的矩阵创建一个文件，然后使用包含翻转键和标题的第二个文件覆盖它？我不能遵循逻辑。

我已经更新了操作系统，R，RStudio版本，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，下面是示例矩阵：

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()

我真的很感谢对此问题的任何见识。

Answer 1

我认为这是由于我不仅仅拥有1到4个元素，因为我添加的彩色行被算作必须在显示矩阵中排列的其他元素。

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。经过一番努力，我终于设法使以下布局生效（根据我的实际数据，而不是我的示例数据）。

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),

请注意包含元素5和6。

所以我的最终命令如下所示（请注意，还会有许多其他更改，但是真正的进步是在我添加了5和6之后发生的）：

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() 

此外，如果您不是每次都通过创建PNG来启动，而每次都不是通过使用dev.off()来启动，那么它将不起作用。我相信这也可能是造成我困惑的原因，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（和我的矩阵一起）创建了这张图片。

我所做的是一种真正的标记块的游戏方式，但是在我弄清楚如何使ComplexHeatmap正常工作之前，我会被Heatmap.2这样的黑客所困扰。