Hello everyone,

I have problem with visualizing data with R heatmap()

Here is the input file:

test <- read.table("test.txt", header=TRUE)
head(test)
#       mir503_2 mir503_3   mir542_3 mir542_4 mir450a_1     log2fc
#Amer2        NA       NA         NA       NA        NA -1.7838786
#Wisp1        NA       NA         NA       NA        NA -1.6112954
#Fzd6         NA       NA         NA       NA        NA -1.3792360
#Ccnd1 -1.226608       NA         NA       NA        NA -1.2266078
#Fzd3         NA       NA -0.8968408       NA        NA -0.8968408
#Fzd5         NA       NA         NA       NA        NA -0.8275608

Then i ordered by log2fc

test_order <- test[order(test$log2fc),]

rownames(test_order) 

[1] "Amer2"   "Wisp1"   "Fzd6"    "Ccnd1"   "Fzd3"    "Fzd5"    "Sfrp1"   "Nxn"     "Wnt4"

Then I picked specific columns:

test_selected_columns<- test_order[,1:6]
test_selected_columns <- as.matrix(test_selected_columns)

Now lets plot

library("RColorBrewer")

col<- colorRampPalette(c("red", "violet", "blue"))(256)

heatmap(test_selected_columns, Rowv=NA, Colv=NA, col = col, 
                                              #xlab="something", 
                                              ylab="",na.rm = TRUE, 
                                              main="title",scale="column", margins=c(5,10))

But I got this plot!

How can fix this issue? I used as.matrix() but it doesn't work?

Thank you