How to get the order of the gene list and indivdual cluster from the big heatmap made by heatmap2.0?
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@shuvadeepmaity-19471
Last seen 2.5 years ago

I hav a data set with expression of around ~8000 genes with 2 replictes and two conditions Now I plotted the heatmap using heatmap2 with row clusterring (see below)

> y <- read.csv('test.CSV', row.names = 'Gene_name', header = T)
> head(y)
                    R1_12      R2_12       R1_36        R2_36
1110004E09Rik  0.02448855  0.1928913  0.10312804 -0.243083469
2010300C02Rik  0.03967733  0.1089108  0.23843350  0.589653327
2210016F16Rik -0.01678531 -0.1019228 -0.31759875 -0.282965985
2410002F23Rik -0.05737916 -0.1057968 -0.07236606 -0.005287509
2700097O09Rik  0.07958317  0.1220447  0.22541512 -0.004510939
4931406P16Rik -0.07985068 -0.1200976 -0.05551624 -0.030421710

> hr <- hclust(as.dist(1-cor(t(y), method="pearson")), method="complete")
> my_palette <- colorRampPalette(c("blue", "white", "red"))(n = 299)
> mycl <- cutree(hr, k=25)#define the number of cluster
> mycolhc <- rainbow(length(unique(mycl)), start=0.1, end=0.9)
> mycolhc <- mycolhc[as.vector(mycl)]
> heatmap.2(as.matrix(y), Rowv=as.dendrogram(hr), Colv= NULL, scale="row", density.info="none", trace="none",col=my_palette, margins =c(10,6),RowSideColors=mycolhc)

and it successfully plotted nice heatmap.

I used RowSideColors to define my cluster and I can extract the clusters using cuttree.

How do I know/ extract the name and order of the genes similar to the order as displayed in the heatmap? The ordering is important for further analysis.

annotation heatmap • 312 views
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@james-w-macdonald-5106
Last seen 3 hours ago
United States

The function heatmap.2 isn't part of Bioconductor, so this isn't the right venue for your question. In future, please ask about CRAN packages at r-help@r-project.org.

And you could have already answered your own question by simply reading the help page for this function! From ?heatmap.2:

Value:

     Invisibly, a list with components

  rowInd: row index permutation vector as returned by
          order.dendrogram.

  colInd: column index permutation vector.

And the only trick here is to know that something returned invisibly isn't normally returned unless you capture it in an object:

> z <- heatmap.2(matrix(rnorm(100), 10))
> z$rowInd
 [1]  2  6  3  5  7  8  1  4  9 10
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