Two-dimensional hierarchically clustered heatmap
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19 months ago

Dear Scientist, I respectfully would like to get your feedback(tutorial) on the following questions. I have gene expression data from the same Biological replicates of two tissues of the brain(cortex and cerebellum) I want to know if Cortex and Cerebellum genes have similarities in their expression/co-expressed/ for the condition I am studying. I did data normalization using DESeq2. Then, I break the data into two(cortex and cerebellum) for correlation analysis. Now, my question is: (1) How could I extract a cluster of correlated genes between the cortex and cerebellum from the two-dimensional hierarchically clustered heatmap for further analysis? (2) How I could assign color bars for the different clusters of genes in the rows and columns-here theoretically asking color assignment for each cluster in the rows and columns as indicated in WGCNA approach.
Here simulated the data as follow.

## Cortex expression profile
set.seed(123)
cortex = matrix(rnorm(1000, 2), 100, 10)
rownames(cortex) = paste0("gene_", 1:100)
colnames(cortex) = LETTERS[1:10]

## cerebellum expression profile
set.seed(177)
cerebellam = matrix(rnorm(1000, 2), 100, 10)
rownames(cerebellam) = paste0("gen_", 1:100)
colnames(cerebellam) = LETTERS[1:10]

## similarity measure
Tissue_corrlation = cor(t(cortex), t(cerebellam))

##Heatmap
library(ComplexHeatmap)
Heatmap(Tissue_corrlation ,cluster_rows = as.dendrogram(hclust(dist(Tissue_corrlation))),
cluster_columns = as.dendrogram(hclust(dist(t(Tissue_corrlation )))))


Thank you!

heatmap cluster corrlation R • 424 views
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Extracting genes or regions per cluster has been asked before

and

https://github.com/jokergoo/ComplexHeatmap/issues/136

For question two please read the manual, I guess the Heatmap Decoration section is relevant: https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html