I expected the same pattern but here I am not able to compare the patterns as the order of genes does not seem the same. I mean how I can have two heat maps on which the order of genes are the same so I woulds be able to compare the block of yellow and blue colors in two heat maps.
I have used this code
require("RColorBrewer")
myCol <- colorRampPalette(c("dodgerblue", "black", "yellow"))(100)
myBreaks <- seq(-2, 2, length.out=101)
heat <- t(scale(t(sc_DEGG)))
hr <- hclust(as.dist(1-cor(t(y), method="pearson")), method="complete")
heatmap.2(
heat,
Rowv=as.dendrogram(hr),
Colv=as.dendrogram(hc),
col=myCol,
breaks=myBreaks,
main="Title",
key=T,
keysize=1.0,
scale="none",
density.info="none",
reorderfun=function(d,w) reorder(d, w, agglo.FUN=mean),
trace="none",
cexRow=0.2,
cexCol=0.8,
distfun=function(x) dist(x, method="euclidean"),
hclustfun=function(x) hclust(x, method="ward.D2")
)
I have made a pair of heat maps based on your code in complexheatmap package. The right heat map is lighter than the left one. I don't know which one has been clustered based on the another one. How I can make the right one darker so that both seem more similar??