Dear members,

I was running oncoPrint function of ComplexHeatmap package and I got the following:

library(ComplexHeatmap)

mat = read.table(textConnection(

  "\tS1\tS2\tS3

  Gene_1\t\t\tMUT;HOMDEL

  Gene_2\tMUT\tMUT\tMUT

  Gene_3\t\tHOMDEL\t

  Gene_4\t\t\t\

  Gene_5\t\tAMP\t     

"), row.names = 1, header = TRUE, sep = "\t", stringsAsFactors = FALSE)

mat <- as.matrix(mat)

alter_fun_list = list(

  background = function(x, y, w, h) {

    grid.rect(x, y, w-unit(0.5, "mm"), h-unit(0.5, "mm"), gp = gpar(fill = "#CCCCCC", col = NA))

  },

  HOMDEL = function(x, y, w, h) {

    grid.rect(x, y, w-unit(0.5, "mm"), h-unit(0.5, "mm"), gp = gpar(fill = "blue", col = NA))

  },

  AMP = function(x, y, w, h) {

    grid.rect(x, y, w-unit(0.5, "mm"), h-unit(0.5, "mm"), gp = gpar(fill = "red", col = NA))

  },

  MUT = function(x, y, w, h) {

    grid.rect(x, y, w-unit(0.5, "mm"), h*0.33, gp = gpar(fill = "#008000", col = NA))

  }

)

col = c("MUT" = "#008000", "AMP" = "red", "HOMDEL" = "blue")

oncoPrint(mat, alter_fun_list = alter_fun_list, col = col, heatmap_legend_param = list(title = "Alternations", at = c("AMP", "HOMDEL", "MUT"), labels = c("Amplification", "Deep deletion", "Mutation")))

Error in oncoPrint(mat, alter_fun_list = alter_fun_list, col = col, heatmap_legend_param = list(title = "Alternations",  :  You should define shape function for: MUT;HOMDEL

It works when I set only MUT or HOMDEL

I would like to know how to create this graphic when I have two events together (MUT and HOMDEL for exemple). 

Thanks for help,

Here is the session info

> sessionInfo()

R version 3.2.2 (2015-08-14)

Platform: x86_64-apple-darwin13.4.0 (64-bit)

Running under: OS X 10.9.5 (Mavericks)

locale:

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:

[1] grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:

[1] ComplexHeatmap_1.6.0

loaded via a namespace (and not attached):

 [1] colorspace_1.2-6    rjson_0.2.15        magrittr_1.5        circlize_0.3.3      tools_3.2.2         whisker_0.3-2      

 [7] GlobalOptions_0.0.8 RColorBrewer_1.1-2  GetoptLong_0.1.1    shape_1.4.2         dendextend_1.1.2