heatmap.2 function from glpot issue

Question

[1769mkc]

my heatmap with gplot I have been trying heatmap with gplot as i wanted to get a zscore in my plot, i use pheatmap but since it doesn't give that zscore thing ,I'm trying to use glpot library ,here is my code i can't get the dimension right either the sample names are missed or the gene ID

library(gplots)
file1<- read.csv('new_dev.txt',header = T)
class(file1)
dat <- data.frame(file1)
dim(dat)
names(dat)
head(dat)
rownames(dat) <-dat$gene
head(dat)
dim(dat)
head(dat)
dat.tdy <- dat[,2:6]
dat.n <- scale(t(dat.tdy))
dat.tn <- t(dat.n)
round(colMeans(dat.n),1)
apply(dat.n,2,sd)
d1 <- dist(dat.n,method = "euclidean", diag = FALSE, upper = FALSE)
d2 <- distdat.tn,method = "euclidean", diag = FALSE, upper = TRUE)
c1 <- hclust(d1, method = "ward.D2", members = NULL)
# Clustering distance between proteins using Ward linkage
c2 <- hclust(d2, method = "ward.D2", members = NULL)

macolor = colorRampPalette(c("navyblue", "white", "red"))(100)


row_names <- rownamesdat.tn)

heatmap.2dat.tn, Rowv=as.dendrogram(c2),col =macolor 
          ,scale="row", margin=c(3.1, 5),trace='none',labRow = row_names,
          symkey=FALSE,symbreaks=FALSE,dendrogram="both",  
          density.info='density', denscol="red",lhei=c(1,2),
          lwid=c(1,1), keysize=0.1, key.par = list(cex=0.5))

dev.off()

Any suggestion or improvement would be highly appreciated.

Answer 1

[Kevin Blighe]

Have you looked through my innumerous postings on heatmap.2, pheatmap, and Heatmap (from ComplexHeatmap)?

I would recommend scaling your data outside the heatmap.2 function, setting breaks, and specifying a reordering function:

heatZ <- t( scaletdat.tn)) )
myBreaks <- seq(-3, 3, length.out=101)
heatmap.2(
  data.matrix(heatZ),
  ...,
  breaks=myBreaks,
  scale="none",
  reorderfun=function(d,w) reorder(d, w, agglo.FUN=mean), ...)

You can also play around with different distance and linkage methods:

#Re-order rows/columns by mean, use 1-Pearson's correlation distance, and complete linkage
heatmap.2(
  ...,
  reorderfun=function(d,w) reorder(d, w, agglo.FUN=mean),
  distfun=function(x) as.dist(1-cor(t(x))),
  hclustfun=function(x) hclust(x, method="complete"))

#Re-order rows/columns by mean, use Euclidean distance, and Ward's linkage
heatmap.2(
  ...,
  reorderfun=function(d,w) reorder(d, w, agglo.FUN=mean),
  distfun=function(x) dist(x, method="euclidean"),
  hclustfun=function(x) hclust(x, method="ward.D2"))

---

See these threads:

heatmap.2

• A: heatmap.2 row clustering does not look right
• A: How to cluster the upregulated and downregulated genes in heatmap?
• A: Hierarchical Clustering in single-channel agilent microarray experiment

pheatmap

• A: extract dendrogram cluster from pheatmap

ComplexHeatmap

• C: how to cluster genes in heatmap
• A: Hierarchical Clustering in single-channel agilent microarray experiment

[1769mkc]

so the graphics issue is due to the scaling promlem because i tweaked margin the lhei ,lwid etc okay i will go through it