Hi All,
I generated the attached heatmap using the following R code and attached
testfile.
I tried to move the legend to the bottom, Can anyone help me? I have played
for 3 hours and can not resolve the problem.
I realized that in the last email, I forgot to include the "Group" variable for
legend. I added to the R code below.
Thank you,
Ding
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png("heatmaps_test2.png", # create PNG for the heat map
width = 5*300, # 5 x 300 pixels
height = 5*300,
res = 300, # 300 pixels per inch
pointsize = 8 # smaller font size
)
# lmat = rbind(c(0,0,4),c(3,1,2),c(0,0,5))
# #1. RowSideColors;2.Heatmap;3.Row tree;4.Column tree;5.Color key
# lwid = c(0.8,0.15,7) # lwid controls the column width # lhei = c(0.1,5.5,1)
#lhei controls the row height
my_palette2 <- colorRampPalette(c("blue", "cyan4", "red"))(n = 299) col_breaks
= c(seq(-1.5,-1.1,length=100), # for bllue
seq(-1.099,1.099,length=100), # for green
seq(1.1,1.5,length=100)) # for red cols <- c("red", "black",
"blue") heatmap.2(as.matrix(testfile), key=T,
#lmat=lmat, lwid=lwid, lhei=lhei,
symkey=FALSE,#keysize=1, key.par =list(cex=0.25),
key.xlab="Heatmap color key",
key.title =" ",
RowSideColors= cols[as.numeric(as.factor(allinfo.blood$Group))],
density.info="none", # turns off density plot inside color legend
trace="none", # turns off trace lines inside the heat map
col=my_palette2, # use color palette defined earlier
breaks=col_breaks,
cexRow=1.4,
labCol=" ", # default to colnames(x)
#labRow=" ",
#margins =c(12,9),
#Colv="NA", # only draw a row dendrogram
hclust=function(x) hclust(x,method="complete"),
distfun=function(x) as.dist((1-cor(t(x)))/2)
) # using pearson correlation as distance
Group <-c("Blood: Vector", "Blood: Vector", "Blood: E2", "Blood: E2",
"Blood: E2+BP3", "Blood: E2+BP3", "Blood: Vector", "Blood: Vector",
"Blood: E2", "Blood: E2", "Blood: E2+BP3", "Blood: E2+BP3")
groups = levels(as.factor(Group))
legend(0.2,0.1, groups, col=cols, pch=15, ncol = 3, cex=1)
dev.off()
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