零件缺少的零件，然后重新出現並覆蓋保存時的整個圖？ （R，Heatmap.2）

Question

我正在使用heatmap.2來創建一個繪圖，但是，保存到我的源文件夾的初始繪圖缺少一個鍵和標題。

然后，當我運行dev.off()命令時，Key和Title會用於覆蓋原始圖形嗎？

例如，我將生成這樣的情節：

這遠非完美。 但是當我運行dev.off()來關閉設備時（否則會出現許多其他錯誤）：

你在上面看到的是一個非常扭曲的Key和我的'XYZ'標題。

為什么它在創建兩個文件，首先是我的矩陣文件，然后用包含我的翻轉鍵和標題的第二個文件覆蓋它？ 我無法遵循邏輯。

我已經更新了我的操作系統，我的R版本，RStudio，我的所有軟件包以及未安裝的RStudio。 似乎沒有任何幫助。

如果您想嘗試復制我的錯誤，請參見示例矩陣：

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))

這是我用來繪制示例數據的腳本。 您需要提供SourceDir並確保將矩陣分配給名稱“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()

我非常感謝對這個問題的任何見解。

Answer 1

我相信這是因為我不僅僅有1到4個元素，因為我添加的彩色行計為必須在顯示矩陣中排列的附加元素。

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))

不再切黃油。 經過多次努力，我終於設法讓以下布局工作（根據我的實際數據，而不是我的示例數據）。

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),

請注意包含元素5和6。

所以我的最終命令看起來像這樣（注意會有很多其他的變化，但是一旦我在5和6中添加了真正的進展）：

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過使用dev.off()創建PNG和enf來dev.off()它將無法工作。 我相信這也可能對我的困惑有所貢獻，並且可能在繪制熱圖后，一旦運行dev.off（）命令就會繪制一些元素，從而導致熱圖被覆蓋。

這（使用我的矩陣）創建此圖像。

我所做的是一種真正的gammy方式來標記我的塊，但直到我能弄清楚如何使ComplexHeatmap正常工作我將被困在使用Heatmap.2這樣的黑客。