Question: RNA-seq heatmap output order
0
gravatar for Sathish
2.8 years ago by
Sathish60
India
Sathish60 wrote:

I am trying to make make heat map for my data set using cluster 3.0 program. I am looking to get output by gene order which was in my input file. Could you let me know how to visualize results in gene order based on input data. The input data from RNA-seq FPKM values.

heatmap rna-seq cluster 3.0 fpkm • 1.0k views
ADD COMMENTlink modified 2.8 years ago by Rashedul Islam370 • written 2.8 years ago by Sathish60

Just a suggestion: why not use R Programming Language for this? ( see A: Heatmap based with FPKM values ). It is then possible to maintain the order as per your original data by switching to off the row dendrogram with the Rowv=FALSE argument.

One can also use Heatmap from ComplexHeatmap ( C: Hierarchical Clustering in single-channel agilent microarray experiment ) and specify row or column ordering by supplying a vector of the desired gene / sample names, as per your desired ordering. For example row_order=rownames(MyDataMatrix) will order as per your data.

Kevin

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by Kevin Blighe66k
1

Thanks for comments. I have fixed the above issue and will check about R program.

ADD REPLYlink written 2.8 years ago by Sathish60
0
gravatar for Rashedul Islam
2.8 years ago by
Canada
Rashedul Islam370 wrote:

One example R code using pheatmap.

library(pheatmap)

Input data

data = matrix(rnorm(200), 10, 10)
rownames(data) = LETTERS[1:10]
colnames(data) = letters[1:10]

Stop clustering of rows to keep name orders according to the input.

pheatmap(data, cluster_rows = F)

ADD COMMENTlink written 2.8 years ago by Rashedul Islam370
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1507 users visited in the last hour