CODEWITHSUNDEEP
rexpressionheatmap
pali
pali

Reputation: 305

How to make color break in Complexheatmap package

I am trying to creat a heatmap using complexheatmap package. Everything is working except that I can see only black color throughout the plot. I think proper colour break should do the trick but I don't know how to fix this :(

#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"))

)

and 

min(zzz)

gave -1.96339 while 

max(zzz)

gave 9.238137. My final plot look like this

enter image description here

test data can be found HERE

Upvotes: 0

Views: 1783

Answers (1)

Zuguang Gu
Zuguang Gu

Reputation: 1321

I think you should remove "rect_gp = gpar(col = "black")" because I guess you have many rows in matrix that the color will be mainly covered by the cell borders if the border color is set.

Upvotes: 1

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