如何在 Complexheatmap 包中进行颜色中断

Question

我正在尝试使用 complexheatmap 包创建热图。一切正常，除了我在整个情节中只能看到黑色。我认为适当的颜色中断应该可以解决问题，但我不知道如何解决这个问题:(

#load required libraries
 library(extrafont)
 #font_import() # only one time required when first time use the      library       extrafont
 #y
 fonts() 
 loadfonts()
 library(ComplexHeatmap)
 library(circlize)

  #upload expression data
  #heatdata<- read.table("probe.expression",header=TRUE,row.names=1)
  dim(heatdata)
  head(heatdata)

#scale row
rm <- rowMeans(heatdata)
sx <- apply(heatdata, 1, sd)
zz <- sweep(heatdata,1,rm)
zz <- sweep(zz, 1, sx, "/")
zzz <- t(scale(t(heatdata)))


Heatmap(zzz, 
name = "Color key", # legend title
rect_gp = gpar(col = "black"), # cell border
column_title = "Tissue",
column_title_side = "top",
row_title = "Genes",
row_title_side = "left",
clustering_distance_rows = "pearson", #"euclidean", "maximum", "man-
                                  #hattan", "canberra", "binary", "minkowski", #"pearson",                             #"spearman", "kendall"                                 
row_dend_side = "left",  #should the row cluster be put on the left or right of the heatmap?
 #row_name_side = "right",  #should the row cluster be put on the left or right of the heatmap?
show_row_names = FALSE,
column_dend_height = unit(3,"cm"),
show_column_dend = FALSE,
show_column_names= FALSE,
#bottom_annotation = ha,
#bottom_annotation_height = unit(1, "cm"),
col = colorRamp2(c(-2, 0,10),c("green","black", "red"))

)

和

min(zzz)

给出 -1.96339 而

max(zzz)

给了 9.238137。我的最终情节是这样的

可以查到测试数据HERE

Answer 1

我认为你应该删除 "rect_gp = gpar(col = "black")" 因为我猜你在矩阵中有很多行，如果设置了边框颜色，颜色将主要被单元格边框覆盖。

如何在 Complexheatmap 包中进行颜色中断

How to make color break in Complexheatmap package

expression

r

heatmap