【R】 heatmap.2()参数

gplots (version 3.1.1)

heatmap.2: Enhanced Heat Map

This heatmap provides a number of extensions to the standard R heatmap function.

heatmap.2 (x,
           # dendrogram control
           Rowv = TRUE,
           Colv=if(symm)"Rowv" else TRUE,
           distfun = dist,
           hclustfun = hclust,
           dendrogram = c("both","row","column","none"),
           reorderfun = function(d, w) reorder(d, w),
           symm = FALSE,

           # data scaling
           scale = c("none","row", "column"),
           na.rm=TRUE,

           # image plot
           revC = identical(Colv, "Rowv"),
           add.expr,

           # mapping data to colors
           breaks,
           symbreaks=any(x < 0, na.rm=TRUE) || scale!="none",

           # colors
           col="heat.colors",

           # block sepration
           colsep,
           rowsep,
           sepcolor="white",
           sepwidth=c(0.05,0.05),

           # cell labeling
           cellnote,
           notecex=1.0,
           notecol="cyan",
           na.color=par("bg"),

           # level trace
           trace=c("column","row","both","none"),
           tracecol="cyan",
           hline=median(breaks),
           vline=median(breaks),
           linecol=tracecol,

           # Row/Column Labeling
           margins = c(5, 5),
           ColSideColors,
           RowSideColors,
           cexRow = 0.2 + 1/log10(nr),
           cexCol = 0.2 + 1/log10(nc),
           labRow = NULL,
           labCol = NULL,
           srtRow = NULL,
           srtCol = NULL,
           adjRow = c(0,NA),
           adjCol = c(NA,0),
           offsetRow = 0.5,
           offsetCol = 0.5,
           colRow = NULL,
           colCol = NULL,

           # color key + density info
           key = TRUE,
           keysize = 1.5,
           density.info=c("histogram","density","none"),
           denscol=tracecol,
           symkey = any(x < 0, na.rm=TRUE) || symbreaks,
           densadj = 0.25,
           key.title = NULL,
           key.xlab = NULL,
           key.ylab = NULL,
           key.xtickfun = NULL,
           key.ytickfun = NULL,
           key.par=list(),

           # plot labels
           main = NULL,
           xlab = NULL,
           ylab = NULL,

           # plot layout
           lmat = NULL,
           lhei = NULL,
           lwid = NULL,

           # extras
           extrafun=NULL,
           ...
           )

Arguments

1. x 矩阵数据

   library(gplots)
   mat <- matrix(data = c(0.1, 0.3, 0.4, 0.6,
                          0.2, 0.5, 0.7, 0.8,
                          0.9, 0.15, 0.25, 0.35,
                          0.4, 0.55, 0.65, 0.75), ncol = 4, nrow = 4)
   
   heatmap.2(mat)
   

   

2. Rowv默认为TRUE，即画出行树状图，且如果是整数向量，则根据向量的顺序计算并重新排序。若为FALSE,则不给出树状图且不重新排序。

3. Colv与Rowv相同，若输入为方阵，还可以设置Colv = Rowv表明相同设置

   heatmap.2(mat, Rowv = F, Colv = F)
   

   

4. distfunc用于计算行和列之间的距离（相异性）的函数，默认dist

5. hclustfun当 Rowv 或 Colv不是树状图时，用于计算层次聚类的函数，默认为 hclust

6. dendrogram绘制树状图，参数可以是none,both,column,row，当与Rowv和Colv参数冲突时，以Rowv和Colv为准

7. reorderfun

8. symm对称，只有当x为方阵时才有可能设置为TRUE

9. scale

10. na.rm

11. revC

12. add.expr

13. breaks设置key的范围

    heatmap.2(mat, Rowv = F, Colv = F,
              breaks = seq(0,1,0.04))
    

    

14. symbreaks

15. col热图颜色设置

    coul <- colorRampPalette(brewer.pal(8, "PiYG"))(25)
    coul2 <- colorRampPalette(brewer.pal(9, "Purples"))(25)
    heatmap.2(mat, Rowv = F, Colv = F,
              breaks = seq(0,1,0.04),
              col=coul)
    heatmap.2(mat, Rowv = F, Colv = F,
              breaks = seq(0,1,0.04),
              col=coul2)
    

    
    

16. colsep, rowsep, sepco

17. sepwidth

18. cellnote 块里加上数字

19. notecex note的大小

20. notecol note的颜色

    heatmap.2(mat, Rowv = F, Colv = F,
              breaks = seq(0,1,0.04),
              col=coul2,
              cellnote = mat,
              notecol = "black",
              notecex = 2)
    

    

21. na.color NA值的颜色

22. trace

23. tracecol

24. hline, vline, linecol

25. margins

26. ColSideColors 长度为 ncol (x) 的字符向量，其中包含可用于标注 x 的列的水平边条的颜色名称。

27. RowSideColors 同 ColSideColors

    heatmap.2(mat, Rowv = F, Colv = F,
              breaks = seq(0,1,0.04),
              col=coul2,
              cellnote = mat,
              notecol = "black",
              notecex = 2,
              RowSideColors = c("red","blue","red","blue"),
              ColSideColors = c("red","blue","red","blue")
    )
    

    

28. cexRow, cexCol

    heatmap.2(mat, Rowv = F, Colv = F,
              breaks = seq(0,1,0.04),
              col=coul2,
              cellnote = mat,
              notecol = "black",
              notecex = 2,
              cexRow = 4,cexCol = 4
    )
    

    

29. labRow, labCol重新设置坐标轴名称

    heatmap.2(mat, Rowv = F, Colv = F,
              breaks = seq(0,1,0.04),
              col=coul2,
              cellnote = mat,
              notecol = "black",
              notecex = 2,
              cexRow = 2,cexCol = 2,
              labRow = c("A","B","C","D"), labCol = c("E","F","G","H")
    )
    

    

30. srtRow, srtCol 行列坐标旋转角度

    heatmap.2(mat, Rowv = F, Colv = F,
              breaks = seq(0,1,0.04),
              col=coul2,
              cellnote = mat,
              notecol = "black",
              notecex = 2,
              cexRow = 2,cexCol = 2,
              labRow = c("A","B","C","D"), labCol = c("E","F","G","H"),
              srtCol = 0 
    )
    

    

31. adjRow, adjCol

32. offsetRow, offsetCol 调整坐标轴标签上下位置

33. colRow, colCol

    heatmap.2(mat, Rowv = F, Colv = F,
              breaks = seq(0,1,0.04),
              col=coul2,
              cellnote = mat,
              notecol = "black",
              notecex = 2,
              cexRow = 2,cexCol = 2,
              labRow = c("A","B","C","D"), labCol = c("E","F","G","H"),
              srtCol = 0,
              colRow = "red", colCol = c("red","blue","green","pink")
    )
    

    

34. key logical indicating whether a color-key should be shown.

35. keysize key大小

36. key.title

37. key.xlab

38. key.ylab

    heatmap.2(mat, Rowv = F, Colv = F,
              breaks = seq(0,1,0.04),
              col=coul2,
              cellnote = mat,
              notecol = "black",
              notecex = 2,
              cexRow = 2,cexCol = 2,
              labRow = c("A","B","C","D"), labCol = c("E","F","G","H"),
              srtCol = 0,
              colRow = "red", colCol = c("red","blue","green","pink"),
              keysize = 1, key.title = "title", key.xlab = "xlab", key.ylab = "ylab"
    )
    

    

39. key.xtickfun

40. key.ytickfun

41. key.par

42. density.info

43. denscol

44. symkey

45. densadj

46. main, xlab, ylab

47. lmat, lhei, lwid 控制plot位置

48. extrafun

R文档
暂时只用到了这些，其余的以后用到补充