R Programming - how to make a simple heat map

Question

[manishamanu5198]

Hi can anyone guide me how to make a simple heat map in R?

[1769mkc]

This one is what helped me and Im sure this will help you as well

A simple tutorial for a complex ComplexHeatmap

[ponganta]

You can make one using various packages (pheatmap, base::heatmap), or you can build one you own using ggplot2::geom_tile. Base R's heatmap is the most versatile function.

Answer 1

[ATpoint]

There is https://github.com/XiaoLuo-boy/ggheatmap which is fully ggplot in case you feel more comfortable with it rather than the suggested pheatmap/ComplexHeatmap packages and want to have a consistent ggplot theme and fonts/sizes/shapes in your plots.

[1769mkc]

will try this

Answer 2

[Friederike]

An excellent tutorial for the pheatmap package is the one by Kamil Slowikowski.

A good overview of the different types of packages and functions that can be used for heatmaps is the one by datanovia. They've basically sorted the packages according to ease of use; the more options one has to tweak individual aspects of the heatmap, the more complex the code gets.

Answer 3

[petrandent]

You can make a heatmap with gplots , this is a great package and you can use Rcolorbrewer for doing better aesthetic graphics.

Answer 4

[benformatics]

I would recommend ComplexHeatmap which in many ways is vastly superior to pheatmap and gplots. The online manual is also extremely extensive.

If you are making a very very simple heatmap you can also do it easily in ggplot2 with geom_tile().

Answer 5

[seidel]

How to make a simple heat map in R:

# define a data set
x <- matrix(rnorm(200), nrow=10, ncol=20)

# add row and column names
rownames(x) <- paste0("g", 1:nrow(x))
colnames(x) <- paste0("c", 1:ncol(x))

# draw a heat map
heatmap(x)

Scaling is on by default with the base heatmap() function. You can turn it off (scale="none"). An easy way to draw prettier heat maps is to call the pheatmap library:

library(pheatmap)
pheatmap(x)

Scaling is off by default, and it draws a legend for the value scale. See the docs as others have pointed out.