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RNA-seq heatmap output order

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.

rna-seq heatmap fpkm cluster 3.0
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updated by Rashedul Islam Rashedul Islam • written by Sathish • Sathish

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

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written by Kevin Blighe Kevin Blighe

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

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written by Sathish • Sathish

1 answer

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)

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written by Rashedul Islam Rashedul Islam

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