Heatmap_custom_dendrogram.rmd

Make a heatmap with colored dendrogram by `complexHeatmap` and `Dendsort`.
See help [here](https://bioconductor.org/packages/release/bioc/vignettes/ComplexHeatmap/inst/doc/s2.single_heatmap.html)
```r
##### a make_hc function to receive different distance_measure and linkage_method
make_hc<- function(x, distance_measure, linkage_method){
        if (distance_measure == "pearson"){
                ## cor calculate for columns, needs to transpose x first
                distance <- as.dist(1-cor(t(x), method = "pearson"))
                hc<- hclust(distance, method = linkage_method)
                
        } else {
        ## dist calculates for rows
        distance<- dist(x, method = distance_measure)
        hc<- hclust(distance, method = linkage_method)
                
        }
        return (hc)
        
}
  
## row is gene
hc_row<- make_hc(mat, "pearson", "complete") 
row_dend<- as.dendrogram(hc_row)
## column is sample

hc_col<- make_hc(t(mat), "euclidean", "complete")
col_dend<- as.dendrogram(hc_col)

## color branches
library(dendextend)

row_dend<- color_branches(row_dend, k = 2)
col_dend<- color_branches(col_dend, k = 3)
Heatmap(mat, name = "foo", cluster_rows = row_dend, cluster_columns = col_dend)

```