Customizing Range Heatmap.2

The heatmap.2 function from the “gplots” package is a popular tool for creating heatmaps in R. While it offers many features and customization options, there are sometimes limitations to achieving specific results. In this article, we will explore how to customize the range of values used in a heatmap.2 plot, including how to achieve a symmetric color scheme that captures the full resolution of your data.

Introduction

The heatmap.2 function is based on the heatmap function from the ggplot2 package, which uses the “gplots” package as an interface. The heatmap.2 function allows users to customize various aspects of the plot, including the colors used, margins, and density information. However, there are times when the default settings may not be sufficient to achieve the desired result.

Scaling Issues

One common issue with heatmap.2 plots is that the data is scaled by row, which can lead to a loss of resolution in the color scheme. This happens because the scale="row" argument scales the data using the minimum and maximum values for each row, rather than preserving the original raw values.

To avoid this scaling issue, we can use the scale="none" argument instead. This will preserve the original raw values, allowing us to maintain the full resolution of our data in the color scheme.

Customizing Color Scheme

Another common request is to customize the color scheme used in a heatmap.2 plot. One way to achieve this is by creating a custom color palette using the colorRampPalette function from the “grDevices” package.

For example, let’s say we want to use a symmetric color scheme that captures the full range of values in our data. We can create a sequence of values from -3 to 3 and set the length.out argument to one more than the number of colors defined. This will ensure that there is always a value for every color in the palette.

Here’s an example code snippet:

heatmap.2(hmdat[select,], scale="none", col = hmcol, trace="none", margin=c(7, 5), cexCol=0.9, cexRow=0.5, density.info="density", breaks = seq(-3, 3, length.out = 101))

In this example, we create a sequence of values from -3 to 3 using the seq function and set the length.out argument to 101. This will result in a color palette with 101 colors, each representing a value between -3 and 3.

Symbreaks Option

One thing to note is that there may be warnings about there being no data for some values when using this approach. To get around this issue, we can use the symbreaks = TRUE argument. This will add breaks to the color palette even if there is no data at those points.

Here’s an updated code snippet:

heatmap.2(hmdat[select,], scale="none", col = hmcol, trace="none", margin=c(7, 5), cexCol=0.9, cexRow=0.5, density.info="density", breaks = seq(-3, 3, length.out = 101), symbreaks = TRUE)

Changing Color Key Labels

Unfortunately, there is no simple option to change the labels of the color key in a heatmap.2 plot. However, we can use workarounds to achieve this.

One possible solution involves modifying the breaks argument to include custom labels. Here’s an example:

heatmap.2(hmdat[select,], scale="none", col = hmcol, trace="none", margin=c(7, 5), cexCol=0.9, cexRow=0.5, density.info="density",
     breaks = seq(-3, 3, length.out = 101),
     main = "Custom Heatmap with Symmetric Color Scheme",
     xlab = "X Axis",
     ylab = "Y Axis")

In this example, we add the main, xlab, and ylab arguments to specify custom labels for the color key.

Conclusion

Customizing a heatmap.2 plot can be challenging, especially when trying to achieve specific results such as a symmetric color scheme that captures the full resolution of your data. By using the scale="none" argument and creating a custom color palette using the colorRampPalette function, we can avoid scaling issues and customize the color scheme to our liking. Additionally, by modifying the breaks argument, we can add custom labels to the color key. While there are limitations to these customization options, they provide a powerful way to create high-quality heatmaps that meet specific requirements.

Last modified on 2025-04-30