Question: Heatmap trouble in R
0
gravatar for Jack
2.4 years ago by
Jack80
Jack80 wrote:

I have a dataset in this format:

id              drug_stat locus   location
5               0          4      755
37133           0         13      755
24086           0          4       41
7               1          4      243
27057           0         13      243
20              1          4      580
21022           1          4      1650

And I want to generate a heat map from it. value1 and value2 are actually the gene's locus type and value2 is location.

my R code for this is the following:

# install libraries
install.packages("gplots")
library(gplots)

# load the dataframe
df <- read.table("data.csv", header = TRUE, sep='\t')
df[df=="n/a"] = NA
df$drug_binary <- ifelse(df$drug_stat == "druggable", 1, 0)
#df[order(df$id_numeric), ]
df_final <- df[c("id_numeric", "drug_binary", "locus_type", "location")]


# change strings to ints for faster read.
df_final$locus_type <- as.numeric(factor(df_final$locus_type))
df_final$location <- as.numeric(factor(df_final$location))

# Plot Heatmap
png(file="plot.png", bg = "transparent")
heat<-heatmap.2(data.matrix(), 
                main = "Sample Heatmap", 
                trace = "none", 
                margin = c(12,30), 
                col = colorRampPalette(c("blue", "yellow", "green")),
                Rowv = NA,
                Colv = NA)

plot(heat)
dev.off()

Question1: Why the binary column is entirely BLUE? It should at least have some GREEN spots in it. Same with the locus.

Question2: Why my plot is not exported as a PNG?

heatmap R • 962 views
ADD COMMENTlink modified 2.4 years ago by ssv.bio180 • written 2.4 years ago by Jack80
0
gravatar for Irsan
2.4 years ago by
Irsan6.8k
Amsterdam
Irsan6.8k wrote:

Because it scales the data. Use the scale="none" option

ADD COMMENTlink written 2.4 years ago by Irsan6.8k
0
gravatar for ssv.bio
2.4 years ago by
ssv.bio180
ssv.bio180 wrote:

Q2:Try adding type="cairo", after file name.

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by ssv.bio180
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