Question: Row label in heatmap
1
gravatar for krushnach80
3.3 years ago by
krushnach80810
krushnach80810 wrote:

I have data frame like this about 250 gene i taking a small subset of it

gene     `WT`           `Treated`
ACTL6A  4.5167211886    4.4304190975
ACTL6B  -4.3730103378 -9.800779238
ACTR5   1.3871253811    1.2086608355

I am plotting heatmap since I m using pheatmap since plotting requires a matrix that is I have to use the only the numeric matrix I m doing something like this rownames(VD3) <- data[,1]

mat <- as.matrix(data[,-1])

I can plot the heatmap but Im missing my gene name labels , How can i include it in my final plot ,any suggestion ?And Im using the pheatmap library

R • 3.1k views
ADD COMMENTlink modified 2.9 years ago by Biostar ♦♦ 20 • written 3.3 years ago by krushnach80810

Can you show the code and output you are getting?

ADD REPLYlink written 3.3 years ago by Deepak Tanwar4.0k
pheatmap(mat,show_rownames=T,col=mycol,breaks=bk,cluster_cols=T,cluster_rows=T,cex=0.9,clustering_distance_rows = "euclidean", clustering_distance_cols = "euclidean", clustering_method = "complete"

+ )

I have no issue in getting the heatmap but it seems that after plotting the gene names are not annotated

ADD REPLYlink written 3.3 years ago by krushnach80810
3
gravatar for theobroma22
3.3 years ago by
theobroma221.1k
theobroma221.1k wrote:

Your code is a bit confusing. You can assign the rownames to the matrix.

Mat = as.matrix( data[,-1])
rownames(Mat) = as.character( data[,1])
head(Mat)
class(Mat)

Did this help you?

ADD COMMENTlink written 3.3 years ago by theobroma221.1k

i will try your suggestion i did figure out

ADD REPLYlink written 3.3 years ago by krushnach80810
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