Question: Heatmap with custom gene labels annotated on the rows
0
gravatar for bioinforesearchquestions
14 months ago by
United States
bioinforesearchquestions280 wrote:

Hi friends,

I would like to generate a heatmap something similar to the below image with custom genes. I am using heatmap.2 function in R.

What parameters should I play with to get the labels as in the image.

Heatmap-with-custom-annotation

ADD COMMENTlink written 14 months ago by bioinforesearchquestions280
1

Have you tried setting the parameter labRow to the value of a vector of rowNames where it contains the names?

..., labRow = rowNames, ...

https://www.rdocumentation.org/packages/gplots/versions/3.0.1.1/topics/heatmap.2

ADD REPLYlink modified 14 months ago • written 14 months ago by Viz40

Thanks, Viz. As you mentioned I gave the specific gene names on the rowNames variable and assigned it to labRow. It is printing only those genes. But the gene names are overlapped. I am trying to fix it and it would be great to have gene name protrude with an arrow.

ADD REPLYlink written 14 months ago by bioinforesearchquestions280
3
gravatar for ATpoint
14 months ago by
ATpoint40k
Germany
ATpoint40k wrote:

I would check out ComplexHeatmap (the 3rd plot at the given link). Yes, it will be work to get your head around the concept of the package but it is well worth it. There is by best knowledge no heatmap package that is more customizable or comprehensive than this one.

ADD COMMENTlink written 14 months ago by ATpoint40k

I am checking out the complex heatmap links. Looks interesting. Thanks for sharing the useful link.

ADD REPLYlink written 14 months ago by bioinforesearchquestions280
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