Understanding Heatmaps: Adjusting Margins for a Better Visual

Introduction to Heatmaps

Heatmaps are a popular visualization tool used in data science and statistics. They provide a graphical representation of data, often displaying values as colors or shades of gray. The heatmap helps us understand patterns and relationships within the data by highlighting areas with high values or correlations.

However, when creating heatmaps, it’s common to encounter issues with margins - particularly at the top and left sides of the plot. These blank spaces can be distracting and detract from the overall visualization. In this article, we’ll delve into the world of heatmap creation and explore ways to adjust margins to improve your visualizations.

Understanding the Basics of Heatmaps

Before we dive into adjusting margins, let’s cover some essential concepts:

• heatmap2 function: The heatmap.2 function in R is used to create heatmaps. It takes various arguments to customize the appearance of the plot.
• par() function: The par() function controls the parameters that affect the overall layout of the plot, including margins.
• svg() function: The svg() function is used to create SVG files, which can be easily shared and embedded in web pages.

The Problem: Blank Space Around Heatmaps

The original code snippet demonstrates a heatmap created using heatmap.2 with some customizations:

svg("mypic.svg", width=20, height=16)
par(mar=c(1,10,0.1,10))
heatmap.2(mat_data_round,
          key = F,
          cellnote = note,     
          notecol="black",      
          density.info="none",  
          trace="none",         
          margins =c(7,14),     
          col=colfun,          
          dendrogram="row",    
          Colv="NA",           
          cexRow=2,
          cexCol=2) 

However, the author encounters issues with blank space around the heatmap due to misaligned margins.

The Solution: Adjusting Margins

To adjust the margins of a heatmap and remove blank space at the top and left sides, you need to specify the margins argument in the heatmap.2 function.

Here’s an example code snippet that demonstrates how to use lwid and lhei arguments:

library(gplots)

data(mtcars)
x  <- as.matrix(mtcars)

# Define margins with lwid and lhei arguments
lwid <- c(0.2,5) # make column of dendrogram and key very small and other column very big 
lhei <- c(0.2,5) # make row of key and other dendrogram very small and other row big

# Create heatmap with adjusted margins
heatmap.2(x,
          key = F,
          dendrogram = "none",
          trace = "none",
          lwid = lwid,
          lhei = lhei)

In this code snippet, lwid and lhei arguments are used to specify the margin sizes for columns and rows, respectively. This adjustment ensures that the heatmap fits perfectly within the plot area.

Additional Considerations

When adjusting margins, keep the following points in mind:

• Marginal values: If you want specific values on the margins (e.g., text labels or titles), make sure to adjust these as well using other par() functions like xpd and main.
• Customization: Experiment with different margin sizes and adjustments until you find a suitable balance between plot space and visualization clarity.

Conclusion

In this article, we explored the importance of margins in heatmap creation. By adjusting the margins argument in the heatmap.2 function using lwid and lhei, you can fine-tune your visualizations to remove blank spaces around the heatmap. Remember to consider other factors like marginal values and customization when making adjustments.

Example Use Cases

1. Visualize temperature distribution across different regions by creating a heatmap with adjusted margins.
2. Create a dendrogram-based visualization for gene expression analysis or network visualization.
3. Develop interactive heatmaps using tools like Plotly, which provide more advanced features and customization options.

By mastering the art of margin adjustment in heatmap creation, you’ll be able to effectively communicate insights from your data visualizations.

Last modified on 2024-10-18