Hi, what i need is as the example i attached in the box plot. As you can
see, the boxplot have margins and it kind
of follow the coding I've added, but, it does not happen for the heat
map. Could you help me with this.. Thanks in advance.
the following is the coding i've used:
# Draw the heatmap
# heatmap.r
#
# Purpose: Create a heatmap
#
# Input: Data matrix as specified in Data-matrix-format.pdf
# Output: Heatmap with dendrograms showing clustering of both
# samples and variables.
# Load necessary libraries, and install them if they are missing
#
tryCatch(library(gplots), error=function(err)
# if this produces an error:
install.packages("gplots",repos="http://cran.ms.unimelb.edu.au/"))
# Prepare the data matrix
par(omi=c(1,1,1,1))
# Read in the .csv file
data<-read.csv("MEAN PERAK RT100 300-399.csv", header = TRUE,
row.names=1)
boxplot(data)
heatmap_data<- data[,-1]
colnames(heatmap_data) <- if
(length(grep("^X[\\d]",colnames(heatmap_data),perl=TRUE)) != 0) #
then
{gsub("^X([\\d].*)","\\1",colnames(heatmap_data),perl=TRUE)}
else
{colnames(heatmap_data)}
# Define palette colours
rch<-rich.colors(256)
rwb<-colorRampPalette(c("red","white","blue"))(256)
rbb<-colorRampPalette(c("red","black","blue"))(256)
pwg<-colorRampPalette(c("purple","white","green"))(256)
pbg<-colorRampPalette(c("purple","black","green"))(256)
pic_onscr<-function(matrix, title="", cex_val=1, pal=rch)
{x11()
heatmap.2(matrix, # matrix to use
#Colv=FALSE, # reorder dendrogram
dendrogram="both", # dendrograms to
draw
col=pal, # palette (see above)
trace="none", # trace line (show
distance)
cexCol=cex_val, # size of column labels
cexRow=cex_val, # size of row labels
key=TRUE, # show the colour key
keysize=cex_val, # key size
density.info="none", # superimpose
"histogram"
or a
# "density" plot on
colour key
margins=c(10,10), # add space for labels
main=title, # title
xlab="", # x-axis title
ylab="" # y-axis title
)
}
# Draw the heatmap
box("plot", col="red")
box("figure", col="green")
par(mar=c(3,2,2,1) + 0.1)
par(omi=c(1,1,1,1))
pic_onscr(t(heatmap_data))
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