Pheatmap or Heatmap3 ?

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4.3 years ago

BioAnna • 0

Hello everyone,

As a newbie in expression data analysis, I would like some information on the heatmap packages in R. My task is to create heatmap from RNA expression data, which belong to 2 groups (2 cancer types).

For that, I've been advised to use heatmap3 or pheatmap package in R.

Could anyone provide some basic information on the main differences in the arguments of these two?

Thank you in advance!

heatmap pheatmap heatmap3 R • 1.6k views

ADD COMMENT • link 4.3 years ago by BioAnna • 0

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Neither. Use ComplexHeatmap - it will save a lot of time when you start adding in new features/requirements to your analysis.

ADD REPLY • link 4.3 years ago by Ram 43k

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I used to use pheatmap, but I agree with @RamRS. ComplexHeatmap brought R heatmaps a needed makeover. You should take a look at the complete reference for ComplexHeatmap to get you started.

https://jokergoo.github.io/ComplexHeatmap-reference/book/introduction.html

ADD REPLY • link 4.3 years ago by frcamacho ▴ 210

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