R Programming - how to make a simple heat map

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


Heatmap


R

• 276 views

There is 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.

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.

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

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.


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