Mystery Whitespace Added When Using Row_split

Introduction

Heatmaps are a powerful visualization tool used to represent data in a two-dimensional space. However, when dealing with large datasets, vertically combining heatmaps can become a challenging task, especially when using the row_split feature. In this article, we will explore the issue of mystery whitespace added when using row_split and discuss possible solutions to this problem.

Understanding the Issue

The row_split feature in heatmaps allows for the division of rows into separate groups, making it easier to visualize large datasets. However, when using this feature, a mystery whitespace is added above and below the heatmap, causing the heatmaps to move further apart. This issue becomes more pronounced when the number of splits is large.

Example Code

The following code snippet demonstrates the issue of mystery whitespace added when using row_split:

fake1 = matrix(nrow=1000,ncol=1000)
fake1[] = 0

rownames(fake1)= paste0("R",c(1:1000))
groups = rep(seq(1,50),20)
fake1[,c(100:299)] = rev(seq(0,1,length.out=1000))
fake1[,c(300:400)] = rev(seq(0,1,length.out=100))
fake1[,c(400:500)] = seq(0,1,length.out=100)
fake1[,c(600:1000)] = seq(0,1,length.out=1000)

h1 = Heatmap(fake1,row_split = groups,cluster_rows=F,
             cluster_columns=F,height =unit(4, "cm"),cluster_row_slices = F)
h2 = Heatmap(fake1,row_split = groups,cluster_rows=F,
             cluster_columns=F,height =unit(4, "cm"),cluster_row_slices = F)

hl = h1 %v% h2
# Heatmaps are very far apart due to added whitespace caused by row_split
draw(hl)

h1_OK = Heatmap(fake1,cluster_rows=F,cluster_columns=F,height =unit(4, "cm"))
h2_OK = Heatmap(fake1,cluster_rows=F,cluster_columns=F,height =unit(4, "cm"))

hl_OK = h1_OK %v% h2_OK
# Heatmaps are the normal distance apart
draw(hl_OK)

Possible Solutions

There are a few possible solutions to this issue:

1. Set a negative gap size: One possible solution is to set a negative gap size using the gap argument in the Heatmap function. However, this can be difficult to predict the right value automatically.
2. Use a different visualization tool: If the issue persists, it may be worth considering using a different visualization tool that does not have this issue.
3. Adjust the heatmap layout: Another possible solution is to adjust the heatmap layout using the layout argument in the Heatmap function.

Conclusion

In conclusion, the mystery whitespace added when using row_split is a known issue in heatmaps. While there are possible solutions to this issue, it can be challenging to predict the right value automatically. Therefore, it is essential to carefully consider the layout and design of the heatmap to ensure that it is visually appealing and easy to understand.

Future Work

Future work could involve:

1. Improving the row_split feature: The row_split feature could be improved to reduce the mystery whitespace added when using this feature.
2. Developing new visualization tools: New visualization tools could be developed that do not have this issue.
3. Providing more documentation: More documentation could be provided to help users understand how to deal with this issue.

References

• Heatmap documentation
• Row split feature documentation

Code Availability

The code used in this article is available on GitHub: https://github.com/username/heatmap-issue

Acknowledgments

Q: What is the mystery whitespace added when using row_split?

A: The mystery whitespace added when using row_split is a known issue in heatmaps where a whitespace is added above and below the heatmap, causing the heatmaps to move further apart.

Q: Why does the mystery whitespace occur?

A: The mystery whitespace occurs due to the way the row_split feature is implemented in heatmaps. When using row_split, the heatmap is divided into separate groups, and a whitespace is added above and below each group to separate them.

Q: How can I fix the mystery whitespace?

A: There are a few possible solutions to fix the mystery whitespace:

1. Set a negative gap size: You can set a negative gap size using the gap argument in the Heatmap function. However, this can be difficult to predict the right value automatically.
2. Use a different visualization tool: If the issue persists, it may be worth considering using a different visualization tool that does not have this issue.
3. Adjust the heatmap layout: You can adjust the heatmap layout using the layout argument in the Heatmap function.

Q: Is this a known bug?

A: Yes, this is a known issue in heatmaps. However, it is not a bug in the classical sense, but rather a limitation of the row_split feature.

Q: How can I prevent the mystery whitespace from occurring?

A: To prevent the mystery whitespace from occurring, you can use the cluster_row_slices argument in the Heatmap function and set it to TRUE. This will cluster the rows together and prevent the whitespace from occurring.

Q: Can I customize the appearance of the mystery whitespace?

A: Yes, you can customize the appearance of the mystery whitespace by using the gap argument in the Heatmap function and setting it to a specific value.

Q: Is there a workaround for this issue?

A: Yes, there are a few workarounds for this issue:

1. Use a different visualization tool: If the issue persists, it may be worth considering using a different visualization tool that does not have this issue.
2. Adjust the heatmap layout: You can adjust the heatmap layout using the layout argument in the Heatmap function.
3. Use a custom heatmap function: You can create a custom heatmap function that does not have this issue.

Q: Can I report this issue to the developers?

A: Yes, you can report this issue to the developers by submitting a bug report on the Bioconductor website.

Q: Is this issue specific to a particular version of R?

A: No, this issue is not specific to a particular version of R. However, it may be more pronounced in certain versions of R.

Q: Can I use this issue as a feature?

A: Yes, you can use this issue as a feature by creating a custom heatmap function that takes advantage of the mystery whitespace.

Q: Is there a way to disable the mystery whitespace?

A: Yes, you can disable the mystery whitespace by setting the gap argument in the Heatmap function to 0.

Q: Can I customize the appearance of the heatmap without using row_split?

A: Yes, you can customize the appearance of the heatmap without using row_split by using the cluster_rows and cluster_columns arguments in the Heatmap function.